(for structural features of involved molecules see the General biochemistry section)

• Schiefferdecker's symbiosis theory : the theory that among the tissues of the body there is a sort of symbiosis, so that the products of metabolism in one tissue serve as a stimulus to the activities of other tissues.

Boehringer-Mannheim "Biochemical Pathways" maps at ExPASy : keyword search

• "Metabolic Pathways" map
• "Cellular and Molecular Processes" map

Medical Biochemistry by M.W.King at Terre Haute Center for Medical Education (THCME), University of Indiana

• as above, integrated at University of Brescia, Italy

Human metabolic pathways of biochemistry (includes DG° values)

Kyoto Encyclopedia of Genes and Genomes (KEGG) : metabolic and regulatory pathways

Main Metabolic Pathways (MMP) on Internet

Metabolic Pathways - Minimaps

Protein Function and Biochemical Pathways (PFBP) Project

WIT/MPW metabolic pathways by Evgeni Selkov

Enzymes and Metabolic Pathways (EMP) database (updated with over 8,000 records a year to cope with the essentials published in the literature each year)

LIGAND (Ligand chemical database for enzyme reactions)

Biomolecular relations in information transmission and expression (BRITE) in the KEGG metabolic pathways

BRENDA (from enzyme to substrate(s) & product(s))

Biocatalysis/Biodegradation Database at University of Minnesota

The ENZYME data bank at ExPASy (EC number, Recommended name, Alternative names, Catalytic activity, Cofactors, Pointers to the SWISS-PROT entrie(s) and disease(s) associated with a deficiency)

BioCarta

Pathways+ (under construction)

Biological Biochemical Image Database (BBID) (pathway images, structures and gene families)

Biomolecular Interaction Network Database (BIND)

Interactive Metabolic Pathways Reports

Klotho (Biochemical Compounds Declarative Database)

Biochemical Pathway Database and Analysis System (BPDAS)

Transpath : gene-regulatory pathways involved in the regulation of transcription factors in man, mouse and rat

Composite regulatory elements in eukaryotes (COMPEL) at Gene REgulatory Sequence Analysis (GRESA)

Database of Interacting Proteins (DIP)

Functional networks (FunkNet) at EML

The metabolic database of soybean genetic database (SoyBase)

Usenet bionet.metabolic-reg

• Lohmann reaction : an easily reversible reaction occurring in muscle, in which the high-energy phosphate bond of ATP is transferred to creatine, forming creatine phosphate; the reaction is catalyzed by creatine kinase
• oxygen debt : the extra oxygen that must be used in the oxidative energy processes after a period of strenuous exercise to reconvert lactic acid to glucose, and decomposed ATP and creatine phosphate to their original states
• nitrogen-containing compounds
• nucleotide metabolism (structural genomics and transcriptomics)
• anabolism
• there have been 11 changes in the part of the DNA that codes for a certain protein subunit of in the electron transport chain known as complex IV / cytochrome oxidase (COX), in the past 58 million years, compared with just one change in the 25 million years before that. None of the rodents, lemurs or other mammals that they examined showed > 2-3 changes in the same time period. These changes could have given human brain cells a serious evolutionary boost, by increasing the amount of energy available to them. Research in modern primates has shown that there is a strong correlation between quality of diet and relative brain size. Humans are an extreme example of this: they have very large brains and a high quality, energy-dense diet^ref
• ATP
• Animated Electron Transport Chain
• Oxidative phosphorylation
• catabolism
• purine catabolism : although purine synthesis and degradation occur in all tissues, urates are produced only in tissues expressing xanthine oxidase, ie mainly liver and small bowel.
• amino acids and proteins (proteomics)
• anabolism :
• visceral proteins
• viscera
• blood cells
• plasma proteins
• catabolism :
• The ubiquitylation pathway^{ref1, ref2}


• cytosolic 26S proteasome / prosome / macropain


It is made up of :
• 1 20S core : 4 stacked rings each containing 7 subunits (total 28 (14 different) subunits).
• first and fourth rings (outer rings) :
• a₁
• a₂
• a₃
• a₄
• a₅
• a₆
• a₇
• second and third rings (inner rings) :
• b₁ / d
• b₂ / Z / z
• b₃
• b₄
• b₅ / MB1 / X
• b₆
• b₈
Assembly and maturation is assisted by chaperon-like proteins (e.g. hsc70 and the proteasome maturation protein (POMP)), which form part of a high molecular weight proteasome precursor complex. Click here for information on immunoproteasomes.
• 2 19S regulator complexes at either ends : it recognizes most of its substrates by a multi-ubiquitin tag (including defective ribosomal products (DRiPs), up to 40% of newly synthesized proteins, representative of self-antigens) and opens the gate of 20S core. Each complex is made up of :
• base, which attaches to the outer ring. It is made up of :
• 2 non-ATPase subunits
• 6 ATPases of the triple-A family (ATP-binding site with Walker A and Walker B motifs) with chaperone-like activity that are believed to help unfold substrates and channel them into the 20S core.
• ATPase 1
• ATPase 2
• ATPase 3
• ATPase 4
• ATPase 5
• ATPase 6
• lid : 8-10 non-ATPase subunits
Degradation of mildly oxidized proteins : the major recognition motif of the substrates seems to be hydrophobic surface patches that are recognized by the 20S core proteasome. Such hydrophobic surface patches are formed by partial unfolding and exposure of hydrophobic amino acid residues during oxidation. Oxidized proteins appear to be relatively poor substrates for ubiquitination, and the ubiquitination system does not seem to be involved in the recognition or targeting of oxidized proteins. Heavily oxidized proteins appear to first aggregate (new hydrophobic and ionic bonds) and then to form covalent cross-links that make them highly resistant to proteolysis
Proteolysis of tightly folded proteins is accelerated greatly when an unstructured region is attached to the substrate. The unstructured region serves as the initiation site for degradation and is hydrolyzed first, after which the rest of the protein is digested sequentially. The initiation site as a novel component of the targeting signal, which is required to engage the proteasome unfolding machinery efficiently. The proteasome degrades a substrate by first binding to its ubiquitin modification and then initiating unfolding at an unstructured region^ref.
See also synthetic proteasome inhibitors
[As functional proteasomes are vital for cell survival (and consequently for viral propagations) viral proteins modulate proteasome activity rather than completely blocking it. E.g. :
• Tax from HTLV-1 interacts with the N3 and C9 subunits
• pX from HBV interacts with C6 subunits
• Nef from HIV-1 interacts with the N3 subunit
• Tat from HIV-1 interacts with the a-rings impairing binding of PA28 but not of the 19S regulator
• E1A from Ad5 interacts with the 19S S4 ATPase subunit]
Web resources :
• 3D structure of proteasome
• Architecture and structure of the proteasome
• Information on the ubiquitin-proteasome pathway of protein degradation
• NetChop Prediction Server : neural network predictions for cleavage sites of the human proteasome
• Prediction Algorithm for Proteasomal Cleavage (PAProC)
• Proteasome Home Page by Cezary Wojcik
• Proteasome structures
• Structures of the yeast proteasome, ubiquitin and related enzymes
• The proteasome : structure and function
• The yeast 20S proteasome
• The yeast 26S proteasome - nomenclature, picture and genes
• Matrix metalloproteinases (MMPs)
• Protein degradation
• metabolites (metabolomics)
• primary metabolites are substances widely distributed in nature, occurring in one form or another in virtually all organisms. In higher plants such compounds are often concentrated in seeds and vegetative storage organs and are needed for physiological development because of their role in basic cell metabolism. As a general rule, primary metabolites obtained from higher plants for commercial use are high volume-low value bulk chemicals.
• secondary metabolites are compounds biosynthetically derived from primary metabolites but more limited in distribution in the plant kingdom, being restricted to a particular taxonomic group (species, genus, family, or closely related group of families). Secondary compounds have no apparent function in a plant's primary metabolism but often have an ecological role; they are pollinator attractants, represent chemical adaptations to environmental stresses, or serve as chemical defenses against microorganisms, insects and higher predators, and even other plants (allelochemics). Secondary metabolites are frequently accumulated by plants in smaller quantities than are primary metabolites. In addition, secondary metabolites, in contrast to primary metabolites, tend to be synthesized in specialized cell types and at distinct developmental stages, making their extraction and purification difficult. As a result, secondary metabolites that are used commercially as biologically active compounds (pharmaceuticals, flavors, fragrances, and pesticides) are generally higher value-lower volume products than the primary metabolites. They often have highly complex structures with many chiral centers which may determine biological activity; such complex compounds cannot be synthesized economically. Genes responsible for the biosynthesis of economically important secondary metabolites have not yet been isolated (for each biosynthetic pathway leading to the production of a secondary metabolite, many genes are required): furthermore, microorganisms routinely used for in vitro production (eg Bacteria) have many enzymes that may catalyze unwanted side reactions with the desired metabolite or intermediates in its biosynthetic pathway. Thus, at least in the immediate future, plants or plant cells will probably continue to serve as the sources for most of these plant-specific materials.
• anaplerotic reaction : a reaction restoring the concentration of crucial intermediates that have been depleted in cellular function.
• carbohydrate metabolism (glycomics)
• anabolism
• Non-glucose-sugar metabolism
• Usenet bionet.glycosci
• catabolism
• aerobic
• anaerobic
• ketone bodies : the substances b-hydroxybutyric acid, acetoacetic acid, and acetone, which are produced by fatty acid and carbohydrate metabolism in the liver in approximately a 78:20:2 ratio. Acetoacetate is produced from acetyl-CoA; most is enzymatically converted to b-ketobutyrate, but a small amount is spontaneously decarboxylated to acetone. The ketone bodies can be used as fuels by muscle and brain tissue. In starvation and uncontrolled diabetes mellitus, large quantities are produced causing metabolic acidosis and elevated blood and urine levels of all 3 ketone bodies.
• Glycolysis
• Crabtree effect : the inhibition of oxygen consumption on the addition of glucose to tissues or microorganisms having a high rate of aerobic glycolysis
• Pasteur effect : the decrease in the rate of glucose utilization (glycolysis) and the suppression of lactate accumulation by tissues or microorganisms in the presence of oxygen
• lipid metabolism (lipidomics / lipomics)
• lipoproteins (see also alterations of lipoprotein metabolism)
• core :
• triglycerids
• esterified cholesterol
• surface (amphipatic molecules) :
• phospholipids
• cholesterol
• apolipoproteins
• apoA-I (in small bowel enterocytes and hepatocytes; in HDL and chylomicrons, activates LCAT). Although there is certainly evidence that cell lines in the fetal human colon1 and in some colon-cancer cell lines^ref synthesize and secrete apolipoprotein A-I, there are no data that demonstrate this capacity in the normal adult colon. Avian species such as chickens synthesize and secrete apolipoprotein A-I from a variety of extrahepatic, extraintestinal tissues^ref, including the colon, but even in chickens, intestinal expression of apolipoprotein A-I mRNA is predominantly restricted to the small intestine. The synthesis of intestinal apolipoprotein A-I in mammals^{ref1, ref2} and, as a corollary, the secretion of pre- HDL cholesterol should be viewed as virtually exclusively confined to enterocytes of the small intestine.
• apoA-II (in small bowel enterocytes and hepatocytes; in HDL and chylomicrons)
• apoA-IV (in enterocytes; in HDL and chylomicrons)
• apoA-V
• apoB (in enterocytes APOBE, a cytidine deaminase made up of a catalytic ....
• APOBEC1
• APOBEC2
• APOBEC3A
• APOBEC3B
• APOBEC3C
• APOBEC3D
• APOBEC3E
• APOBEC3F
• APOBEC3G
... and a regulatory subunit (APOBER1), causes a C=>U transition in codon 2153 (nt 6666 of mRNA) of ApoB mRNA : Gln (CAA) => stop (UAA) substitution allows production of a truncated apoB isoform, termed apoB-48 (found in chylomicrons, binds to apoB-48-R), instead of the apoB-100 produced in hepatocytes (found in VLDL, IDL, and LDL; binds to LDL-R). People who carry the short form of the apoB gene, which occurs only rarely among the very old but commonly among younger adults, have significantly lower levels of LDL cholesterol : changes in how the body responds to cholesterol with age likely explains why the apoB gene can hurt you in old age but save your life in your 40s and 50s.
• apoC-I (hepatocytes; in HDL => chylomicrons, VLDL, IDL)
• apoC-II (hepatocytes; in HDL => chylomicrons => HDL, VLDL, IDL; activator of LPL)
• apoC-III (hepatocytes; in HDL => chylomicrons => HDL, VLDL, IDL; inhibitor of LPL)
• apoD is a 29-kDa glycoprotein that is primarily associated with high density lipoproteins in human plasma. It is an atypical apolipoprotein and, based on its primary structure, apoD is predicted to be a member of the lipocalin family. Lipocalins adopt a b-barrel tertiary structure and transport small hydrophobic ligands. Although apoD can bind cholesterol, progesterone, pregnenolone, bilirubin and arachidonic acid, it is unclear if any, or all of these, represent its physiological ligands. The apoD gene is expressed in many tissues, with high levels of expression in spleen, testes and brain. ApoD is present at high concentrations in the cyst fluid of women with gross cystic disease of the breast, a condition associated with increased risk of breast cancer. It also accumulates at sites of regenerating peripheral nerves and in the cerebrospinal fluid of patients with neurodegenerative conditions, such as Alzheimer's disease. ApoD may, therefore, participate in maintenance and repair within the central and peripheral nervous systems. While its role in metabolism has yet to be defined, apoD is likely to be a multi-ligand, multi-functional transporter. It could transport a ligand from one cell to another within an organ, scavenge a ligand within an organ for transport to the blood or could transport a ligand from the circulation to specific cells within a tissue^ref. It is closely associated with LCAT
• apoE (hepatocytes, macrophages, neurons, glial cells; in chylomicron remnants, VLDL, IDL, HDL; binds to heparan sulfate proteoglycan in Disse space and then to LDL-R or LRPs on hepatocytes; 3 alleles : E2 (12%, lowest affinity for LDL-R), E3 (75%), and E4 (13%); binds to LDL-R and LDLR-related proteins (LRPs))
• apoE-like 1
• apoF
• apoH / b₂ glycoprotein I
• apoJ / clusterin
• apoM is important for the formation of pre-bHDL and cholesterol efflux to HDL, and thereby inhibits formation of atherosclerotic lesions^ref
• apo(a) (hepatocytes; covalent bond to apoB100 in LDLs generates Lp(a); apo(a) competes with thrombin for plasminogen binding, so inhibiting plasminogen conversion to plasmin and facilitating atherosclerosis)
• cytoplasmic apolipoproteins
• apoL1 / trypanosome lytic factor (TLF)
• apoL2
• apoL3
• apoL4
• apoL5
• apoL6

• enzymes in lipoprotein metabolism :
• lipid transfer proteins (LTPs) :
• phospholipid transfer protein (PLTP) is expressed in liver and lungs and support phospholipids to nascent HDLs.
• microsomal triglyceride transfer protein (MTP) transfers triglycerides from the endoplasmic reticulum to apolipoproteins
• cholesteryl ester transfer protein, plasma (CETP) is expressed in hepatocytes and exchanges cholesterol esters from LDLs and HDLs with triglycerids from chylomicrons (after meals) or VLDLs (during fasting), causing the inverse relationship between plasma concentration of HDL-Ch and triglycerids. LDLs are converteed into small dense LDLs.
• ABCA1 transfers free cholesterol from cell membrane to HDL₃
• lecithin:cholesterol acyl transferase (LCAT) is expressed in hepatocytes and binds to HDL; it is activated by apoA-I and apoC-I and esterifies free cholesterol on surface of HDL₃ to linoleic acid in phosphatidylserine (PtS) of HDL : as cholesterol esters move to the core, more free cholesterol can be accepted on surface, and the lipoprotein enlarges to become an HDL₂. As HDLs (on the contrary of IDLs and LDLs) can't penetrate endothelium, they exert a protective effect by moving cholesterol from peripheral tissues to liver
• acylCoA:cholesterol acyltransferases (ACATs) esterifies cholesterol
• ACAT-1 (macrophages)
• ACAT-2 (enterocytes and hepatocytes)
• lipoprotein lipase (LPL) is expressed by adipocytes, skeletal muscle cells, and macrophages (including foamy cells in atherosclerotic lesions, where it can bind and retain LDLs in subendothelial space); secreted in ECM and transported through endothelial cells to bind proteoglycans on lumenal surface; it is activated by apoC-II (and inhibited by apoC-III) and liberates free fatty acids from triglycerids in both chylomicrons (=> remnants) and VLDLs (=> IDLs => LDLs). FFAs are then oxidized in muscle cells or stored in adipocytes. Most circulating LPL is associated with LDL.
• hepatic triglyceride lipase (HTGL) is expressed in hepatocytes and removes triglycerids from
• IDL => large LDL
• large LDL => small dense LDL
• HDL₂ => HDL₃
• apolipoprotein receptors
• scavenger receptor class B, member 1 binds to HDL
• apoB-48-R (on macrophages) binds to apoB-48
• LDL receptor (LDLR) binds to both apoB100 and apoE, and VSV
• LDLR-related proteins (LRPs) bind to apoE and tPA
• LRP / LRP1 / a₂-macroglobulin receptor / CD91 binds to a₂-macroglobulin and is a mitogenic receptor for lactoferrin in osteoblastic cells^ref. LRP, like all members of the LDLreceptor gene family, consists of 5 common structural units:
• ligand-binding (complement) type cysteine-rich repeats
• EGFR–like cysteine-rich repeats
• YWTD domains
• a single membrane-spanning segment
• a cytoplasmic tail that harbors between one and 3 NPxY motifs.
Ligand-binding-type repeats in LRP occur in clusters containing between two and eleven individual repeats. Most of the known ligands for LRP, for which the binding sites have been mapped, interact with these ligand-binding-type domains^ref. These are followed by EGF precursor homology domains, which consist of the two EGF repeats, six YWTD repeats that are arranged in a propeller-like structure^ref, and another EGFrepeat. 6 EGF repeats precede the single membrane-spanning segment. The cytoplasmic tail contains two NPxY motifs that serve as docking sites for the endocytosis machinery and for cytoplasmic adaptor and scaffolding proteins involved in signaling events^ref

Binding of LRP ligands to the different clusters of ligand-binding repeats. Cysteine-rich ligand-binding repeats (red ovals) in LRP are arranged in 4 clusters containing 2, 8, 10, and 11 repeats, respectively. Each cluster is followed by 1–4 EGF homology domains (blue), which consist of cysteine-rich EGF repeats (blue circles) and YWTD domains (wavy line). NPxY motifs in the cytoplasmic tail are indicated by the asterisks. No ligand interactions have been mapped to cluster I. Clusters II and IV bind most of the currently mapped known ligands of LRP. Binding of 2M to clusters II and IV has been found by surface plasmon resonance, although cells transfected with minireceptors containing these clusters do not bind and internalize 2M^ref. ApoE was found to bind to clusters II, III, and IV by ligand blotting. LPL, lipoprotein lipase.
LRP recognizes at least 30 different ligands that represent several families of proteins. These include lipoproteins, proteinases, proteinase-inhibitor complexes, ECM proteins, bacterial toxins, viruses, and various intracellular proteins. By far the largest group of ligands that are recognized by LRP are either proteinases or molecules associated with regulating proteolytic activity. Certain serine proteinases and metalloproteinases bind directly to LRP, while a number of other proteinases only bind once complexed with their specific inhibitors. The latter include members of the Serpin superfamily of serine proteinase inhibitors and the pan-proteinase inhibitors 2M and pregnancy zone protein. These inhibitors are only recognized by LRP following a conformation change that occurs in them after proteolytic cleavage or reaction with small amines. In contrast, LRP recognizes both the native and complexed forms of tissue factor pathway inhibitor (TFPI) (a proteinase inhibitor containing Kunitz-type proteinase inhibitor domains). LRP also binds to the multimeric matrix proteins thrombospondin-1 and thrombospondin-2 and delivers Pseudomonas exotoxin A and minor-group human rhinovirus into cells. In addition, LRP recognizes a number of intracellular proteins, including HSP-96, the HIV-1 Tat protein, and RAP, an endoplasmic reticulum resident protein that functions as a molecular chaperone for LRP and other LDL receptor family members.  A major question that remains unanswered is how LRP can recognize 30 structurally distinct ligands with high affinity. Earlier work with the LDL receptor revealed that the complement-type ligand-binding repeats are responsible for its recognition of ligands; consequently most work has focused on the four clusters of ligand-binding repeats that are present in LRP. Crystallographic and nuclear magnetic resonance studies of individual repeats have revealed that the sequence variability in short loop regions of each repeat results in a unique contour surface and charge density for each repeat^ref. While the locations of the ligand recognition sites for all ligands within LRP are not yet known, two general approaches have been successfully employed to identify the regions responsible for binding a number of ligands. In the first approach^ref, LRP "minireceptors" have been prepared by fusing various clusters of ligand-binding repeats to the LRP light-chain and measuring their ability to mediate the cellular internalization of ligands following expression in cells. In the second approach^ref, soluble recombinant receptor fragments representing each of the clusters in LRP are tested for their ability to bind various known LRP ligands in vitro. Together, these studies have yielded some important insights into the ligand recognition properties of LRP. First, it appears that the major ligand-binding sites within LRP are contained in clusters II and IV; thus far, no ligands besides RAP have been identified that bind to cluster I or cluster III. Interestingly, most ligands bind equally well to both clusters II and IV, suggesting a functional duplication within LRP^ref. Second, deletion analysis reveals that high-affinity binding of most ligands with LRP requires their interaction with multiple ligand-binding repeats. Some ligands, such as a₂M*, appear to bind repeats from two or more clusters. These studies reveal that the ability of LRP to bind numerous structurally distinct ligands with high affinity arises from the presence of 31 ligand-binding-type repeats in the molecule, from the unique contour surface and charge distribution for each repeat, and from multiple interactions between both the ligand and the receptor. Some ligands can recognize different combinations of these repeats in a sequential fashion, while others appear to recognize repeats from separate clusters. Not only does the extracellular domain of LRP bind a multitude of biologically diverse ligands, but there are now also an increasing number of cytoplasmic proteins that have been found to interact with the tail of LRP. A search for such proteins was initiated because it became impossible to reconcile a bewildering spectrum of experimental observations relating to various functions of LRP and other members of the LDL receptor gene family with a simple role as an endocytic receptor or cellular transporter of extracellular ligands. Initially, the search focused on the tetra-amino acid "NPxY" motif that is present in two copies in the LRP tail. Both motifs can independently function as internalization signals. However, one such motif is sufficient to mediate rapid endocytosis of the LDL receptor^ref, suggesting that one or both of these motifs might interact with other proteins in the cytoplasm, in addition to the endocytotic machinery. NPxY motifs had just been shown to interact with cytoplasmic proteins harboring so-called phosphotyrosine-binding (PTB) domains. Furthermore, in an increasing number of cases it became apparent that phosphorylation of the tyrosine residue in these motifs was not required for binding to PTB domains. 2 cytoplasmic, PTB domain–containing proteins were originally described that can interact specifically with the NPxY motifs in the LRP tail. One of these proteins, mammalian Disabled-1 (Dab1), specifically binds the second NPxY motif in the LRP tail and also to equivalent sequences in other LDL receptor family members, and it plays a critical role in the transmission of a positional signal to migrating neurons during brain development^ref. The second such protein, the scaffold protein FE65, contains two PTB domains and one WW domain by which it can specifically interact with LRP^ref, with the amyloid precursor protein (APP)^{ref1, ref2}, and with members of the Ena/VASP family of actin-binding proteins^ref. 2 FE65-like proteins also exist in mammalian species. Both interact via one of their PTB domains with APP^{ref1, ref2}. Whether the other PTB domain in FE65L1 and FE65L2 interacts with LRP has not been tested, but it seems likely.
Ligands that bind the extracellular domain :
• lipoprotein metabolism and transport
• apoE
• lipoprotein lipase
• hepatic lipase
• fibrinolysis, signaling function in brain : tPA
• cell migration, wound healing : uPA
• blood coagulation : factor IXa, VIIIa, VIIa/TFPI
• angiogenesis, metastasis : MMP-9, MMP-13
• sphingolipid activator protein (SAP)
• pan-proteinase inhibitors, infection
• pregnancy zone protein (PZP)
• a₂M
• infection : complement C3
• regulates tPA/uPA activity : PAI-1
• regulates C1r/C1s activity : C1-INH
• regulate blood clotting : antithrombin III, TFPI, heparin cofactor II
• regulates neutrophil elastase : a1-antitrypsin
• physiological role unclear : elastase
• TGF-b activation, matrix cell interactions : thrombospondin-1
• collagen assembly, matrix cell interaction : thrombospondin-2
• Pseudomonas exotoxin A
• antibacterial : lactoferrin
• rhinovirus
• chaperones : RAP, HSP70
• transcriptional activation : HIV-1 Tat protein
Extracellular and intracellular associations of LRP with membrane-bound ligands.
• Left panel: Internalization of GPI-linked or heparan sulfate proteoglycan–linked (HSPG-linked) ligands (examples: uPA:PAI-1, uPA receptor, and apoE-containing lipoproteins). In uPA:PAI-1, PAI-1 binds to LRP and uPA binds to the GPI-linked uPA receptor. ApoE-containing lipoproteins are sequestered on HSPGs, facilitating enrichment with apoE and the interaction with LRP. After internalization and dissociation of the ligands from the receptors in the endosome, receptors recycle to the plasma membrane.
• Middle panel: Association of LRP with APP mediated by the cytoplasmic scaffolding protein FE65. FE65 can interact via independent PTB domains with the LRP and APP tails. The functional significance of this potential cytoplasmic link for APP processing and/or signaling remains to be shown.
• Right panel: Dimerization of LRP by a₂M and association with NMDA receptors (NMDAR). Dimerization of LRP on cultured neurons induces NMDA receptor–mediated Ca²⁺ influx. The postsynaptic density protein PSD-95 interacts with LRP and NMDA receptors through different interaction domains. How precisely NMDA receptors are activated by LRP dimerization is not known at present.

Adapter and scaffold proteins that bind to the intracellular domain :

disabled-1 (Dab-1)	activation of Src family kinases, neuronal migration
FE65	APP processing?, actin remodeling
SEMCAP-1	axon guidance, vesicularr transport?
JIP1, JIP2	regulation of MAPK and SAPK, including JNK
PSD-95	scaffolding protein of the postsynaptic density, coupling to NMDA receptor
talin-like proteins	coupling to actin cytoskeleton
OMP25	mitochondrial transport
CAPON	regulation of nitric oxide synthase
PIP4,5 kinase-like protein	regulation of inositol signaling
ICAP1	integrin-mediated signaling?
Shc	Ras activation

After the initial discovery of Dab1 and FE65 as LRP tail-binding proteins, extensive yeast two-hybrid screens were conducted using different parts of cytoplasmic tails from LDL receptor family members^{ref1, ref2}. Several other gene products were identified that interact specifically with distinct regions in the cytoplasmic tails of LDL receptor family members. Some of these proteins also contain PTB domains^{ref1, ref2, ref3}, which are involved in receptor tail binding, whereas most of the others contain another type of protein interaction structure, PDZ domains. These newly identified adapter and scaffold proteins are key organizers or regulators of MPAK signaling, ion channel function in the postsynaptic density, microtubular transport, nitric oxide signaling, and axon guidance. While specific functions of LRP in most of these processes remain to be determined, it is now clear that LDL receptor family members are involved in at least some of them^{ref1, ref2, ref3}.  When LRP was originally identified, its structural similarity to the LDL receptor and its expression in the liver suggested a role in lipoprotein metabolism and cholesterol homeostasis. Further in vitro evidence that LRP binds apoE led to the proposal that this molecule serves as a receptor for chylomicron remnants, lipoproteins that shuttle primarily dietary cholesterol from the gut to the liver. However, at the same time considerable evidence began to emerge suggesting that a major function of LRP lies in the removal of proteinase and proteinase inhibitor complexes, raising the possibility that LRP may be a multifunctional scavenger receptor. A critical role of LRP, reaching beyond a restricted role in chylomicron remnant transport, was also suggested by gene knockout experiments that revealed an absolute requirement for LRP during the early stages of embryonic development in the mouse^ref. A role for LRP in lipoprotein metabolism has been strengthened by independent findings that revealed that LRP binds not only chylomicron remnants, but also the lipases that are directly involved in the generation of the remnant lipoproteins from triglyceride-rich chylomicrons^ref. Several physiological and genetic studies in mice finally confirmed a function of LRP, in concert with the LDL receptor, in hepatic remnant metabolism^{ref1, ref2, ref3}. LRP is highly expressed not only in the liver, but also in virtually all neurons in the brain. Furthermore, astrocytes abundantly produce apoE in the CNS, raising the possibility that neuronal LRP mediates the neuronal uptake of astrocyte-derived cholesterol and other lipids. Such a function of LRP in the CNS is particularly intriguing in light of the role of apoE in the pathogenesis of late-onset Alzheimer disease and the role of cellular cholesterol content in the processing of APP to the amyloidogenic Aß peptide^ref. Through its effects on certain serine proteinases and metalloproteinases, LRP serves as a crucial regulator of extracellular proteolytic activity. Urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) are serine proteinases that activate plasminogen and play important roles in wound repair, tumor invasion, and cell migration in both normal and pathologic situations^ref. uPA is predominantly cell-associated, interacting with a cellular receptor, uPAR, and it initiates a proteolytic cascade that activates plasminogen to plasmin, which in turn can activate matrix metalloproteinases. This proteolytic pathway is regulated by a specific inhibitor, PAI-1, which forms a stable complex with uPA. Once formed, this complex is rapidly internalized along with uPAR and is degraded in a process mediated by LRP or other LDL receptor family members^{ref1, ref2}. This degradative pathway regenerates unoccupied uPAR, which is necessary to sustain plasminogen activation on the cell surface. Failure to remove uPA:PAI-1 complexes from the cell surface diminishes the capacity for plasminogen activation^ref and may impair the ability of uPA to mediate the removal of PAI-1 bound to vitronectin, thereby inhibiting uPA-dependent cellular migration^ref. Finally, the interaction of uPA with uPAR initiates a variety of intracellular signaling events, such as calcium influx^ref, formation of inositol-3-phosphate^ref, and activation of protein kinases such as the MAP kinase extracellular signal–related kinase (ERK) and its upstream regulator^ref. In addition to its effects on uPA and tPA levels and activity, LRP also regulates levels of certain matrix metalloproteinase (MMP) family members. Barmina et al.^ref demonstrated that the catabolism of collagenase-3 (MMP-13) involves 2 receptors: a specific collagenase-3 receptor that acts as a primary binding site on cells, and LRP, which is required for internalization of this enzyme. Yang et al.^ref found that anti-LRP IgG and RAP can each inhibit adhesion and lead to increased MMP-2 levels in conditioned media from wild-type, but not thrombospondin-2–null, cells, confirming that clearance of MMP-2/thrombospondin-2 complexes is mediated by LRP. Finally, Hahn-Dantona et al.^ref demonstrated a direct high-affinity interaction between MMP-9 and LRP. The ability of LRP to modulate the levels of 3 MMPs (MMP-2, MMP-13, and MMP-9) indicates a major role for this receptor in removing excessive extracellular proteolytic activity. In the case of MMP-9, tight regulation of its activity and levels is important, since this MMP has roles in a variety of processes, including tumor progression and metastasis^ref. LRP levels and activity are known to be substantially decreased in tumors^ref, which would decrease the catabolism of MMP-9 and other proteinases, leading to higher levels of these enzymes at the tumor sites. Of interest in this regard, Kancha et al.^ref observed a correlation between invasive phenotype and low LRP expression in different subclones derived from a tumor cell line, although MMP-9 levels were not measured in these studies. LRP is also indirectly involved in the regulation of the activity of lipid-degrading lysosomal enzymes that require a sphingolipid activator protein (SAP) for activation. Four distinct SAPs (A–D) are generated from a common SAP precursor protein by proteolytic cleavage in the lysosome. Genetic defects in the SAP precursor result in the lysosomal accumulation of several different types of cellular lipids due to enzymatic deficiencies in cerebrosidases, sphingomyelinases, glucosidases, and hexosaminidases^ref. The SAP precursor is transported to the lysosome by two separate pathways involving an intracellular pathway by which SAP is shuttled directly from the trans-Golgi network to the lysosomes and an indirect pathway whereby SAP is first secreted by the cell and then internalized by the same or a neighboring cell. Two different receptor systems mediate SAP transport. Mannose-6-phosphate receptors are involved on one hand, and LRP on the other^ref. Regulation of lysosomal lipid degradative pathways seems to be critical to a cell’s survival, thus providing a rationale for a redundancy in SAP transport mechanisms. As a consequence, only minor accumulations of lysosomal lipids can be detected in LRP-deficient fibroblasts. In the course of evolution, LRP has been hijacked as an entry receptor for a family of viruses and for a bacterial toxin. Minor group rhinoviruses use members of the LDL receptor gene family, not exclusively LRP, as a docking receptor on the cell surface mediating their endocytic uptake into the target cell^ref. Furthermore, a toxin from Pseudomonas aeruginosa, Pseudomonas exotoxin A, enters the cell exclusively via LRP^ref. The latter is a single-chain polypeptide that harbors three distinct functional domains: a receptor-binding domain by which the toxin binds to LRP at the cell surface; a fusogenic domain, which mediates the translocation of the toxin into the cytoplasm; and an enzymatic domain that mediates ADP-ribosylation of elongation factor 2, thereby shutting down protein synthesis in the cell. Recently, a role for LRP in the activation of HIV has also been reported. In this case, LRP was shown to function as a receptor for the HIV-Tat protein, a transactivator for viral genes that is secreted by macrophages and other infected cells in which HIV replicates^ref. The Tat protein binds LRP and thereby becomes internalized. It then leaves the endosomes by a process that is poorly understood and enters the nucleus of the target cells where it stimulates the transcription of dormant viral genes. This process is thought to be of particular importance in the nervous system where LRP is abundantly expressed on neurons and where it may accelerate the dementia that accompanies advanced HIV infection. LRP present in neurons has the capacity to signal and may be involved in long-term potentiation (LTP) and in regulating synaptic plasticity. LTP is an electrophysiological parameter that is widely used to assess the strength and stability of synaptic connections. Such synaptic connectivity patterns are thought to be part of the structural basis for long-term memory. Studies in tPA-deficient mice^ref reveal that late-phase LTP is significantly impaired when compared with that in wild-type mice, and that it can be restored by adding exogenous tPA. The effect of tPA on LTP results from its association with LRP^ref, as RAP inhibits tPA-mediated LTP. tPA has also been reported to potentiate NMDA receptor–mediated neurotoxicity via cleavage of the NR1 subunit of the NMDA receptor, leading to increased activity of the NMDA receptor^ref. Another LRP ligand, a₂M*, associates with neuronal LRP and induces a calcium influx via NMDA receptors^ref, indicating a linkage between LRP and NMDA receptors, which could occur via the multivalent scaffold protein PSD-95. PSD-95 associates with NMDA receptors as well as the cytoplasmic domain of LRP^ref. The influx of calcium due to LRP-mediated activation of NMDA receptor channels is likely to affect a variety of downstream signaling cascades and may provide a mechanism of altering local synaptic plasticity. A number of findings suggest that LRP contributes to the pathobiology of Alzheimer disease (AD). LRP serves as a receptor for APP, apoE, and a₂M, all of which have been genetically linked to AD. Further, the levels of LRP decrease substantially with age^ref, the major risk factor for nonfamilial AD. The contribution of LRP to AD is complex, and studies demonstrate that LRP has the capacity to influence both the production and the clearance of Aß. The association of LRP with forms of APP that contain a Kunitz-type proteinase inhibitor (KPI) domain^ref alters APP processing, leading to increased Aß production^ref. At the same time, the Aß peptide binds avidly to LRP ligands, such as a₂M and apoE, and LRP-mediated clearance of these ligands complexed to Aß contributes to a reduction in Aß levels^{ref1, ref2}. Interestingly, a silent polymorphism in exon 3 of the LRP gene (C776T) is associated with an altered risk for late-onset AD^ref, and significantly lower levels of LRP in the brain have been reported in AD patients with the C/C genotype compared with patients with the C/T or T/T genotype. Decreased LRP expression at clearance sites (perhaps at neurons or at sites along the capillary membranes) could lead to decreased a₂M* and/or apoE-promoted Aß catabolism, resulting in increased Aß deposition. At the same time, increased expression of LRP in activated glia in the AD brain is well documented and could lead to increased Aß production by these cells, also leading to increased Aß deposition. Finally, the signaling roles of LRP in response to ligand binding may be important for normal synaptic plasticity, and loss of LRP function or levels may impair these processes and lead to neuronal degeneration^ref.
• LRP2 / megalin / gp330 / Heymann nephritis antigen
• LRP3
• LRP4
• LRP5 / LRP7
• LRP8
• LRP9
• LRP10
• chicken VLDL/vitellogenin receptor
• Drosophila Yolkless
• chicken LR8B
• placental calcium sensor protein^ref
• apoE receptor 2 (apoER2)^ref
• LR11^ref
These receptors share a similar structure, with a single transmembrane domain and numerous ligand binding domains organized as cysteine-rich repeats arranged in clusters, followed by two epidermal growth factor-like repeats separated from a third one by a spacer region containing a YWTD consensus sequence and an NPXY internalization signal in the cytoplasmic domain.
• during homeostasis, LDL is protected from oxidative modification by HDL-associated enzymes, particularly paraoxonases (1, 2, and 3), which destroys biologically active oxidized phospholipids. During acute phase response (APR) oxidized LDLs are created from small dense LDLs
• anabolism :
• cholesterol is used to ...
• strenghten cell membranes
• synthetise biliary acids
• synthetise steroid hormones
• regulates endogenous cholesterol synthesis
• Fatty acids, triglycerides, phospholipids, sphingolipids and eicosanoids
• 5-lipoxygenase pathway
• LTB₄ metabolism
• 12-lipoxygenase pathway
• 15-lipoxygenase pathway
• Cyclooxygenase pathway I
• Cyclooxygenase pathway II
• Linoleic acid cascade
• Sphingolipids pathway
• catabolism
• Cytochrome P-450 pathway
• Usenet bionet.molecules.p450
• vitamin metabolism
• motility
• inside the cell
• inside the tissues (taxis) : an orientation movement of a motile organism in response to an external stimulus. Such a response may be either positive (toward) or negative (away from the stimulus)
• tropism : the turning, bending, movement, or growth of an organism or part of an organism in response to an external stimulus. Such response may be either positive (toward) or negative (away from the stimulus). By extension, used as a word termination affixed to a stem denoting the nature of the stimulus (phototropism) or the material or entity for which an organism or substance shows a special affinity (neurotropism), usually applied to nonmotile organisms
• chemotaxis : polarized movement in response to gradients (D[ ] in a given Dt) of chemical attractants (e.g. chemotactic cytokines (chemokines) : positive chemotaxis: lengths of the straight runs increase) or repellants (negative chemotaxis: lengths of the straight runs decrease)
• haptotaxis : gradients of substratum-bound substances
Control of cell movements and location by regionalized distribution of adhesive matrix and/or directional signals

(reproduced with permission from Nature Reviews Immunology (Vol 3, No. 11, pp 859-866 (2003)) copyright Macmillan Magazines Ltd)
a : directional cell movement polarized by a chemoattractant gradient (such as a chemokine, green) and facilitated by a suitable matrix for adhesion (mauve grid). However, directional stability of migrating cells does not necessarily require that chemoattractants form a gradient (b)
c : random cell movement that can also result from chemoattractant signalling in the presence of a matrix for adhesion; signals provided by additional chemoattractants (?), if present, might also provide directional information resulting in polarized migration
d : the absence of a suitable matrix for adhesion can limit the regions in which a cell can move, regardless of whether such movement is random or polarized. Given this, the presence of a polarizing signal in the absence of a suitable matrix for adhesion could hypothetically be used to immobilize cells in a given location (e). Although this figure illustrates the reponse to an attractive signal, repulsive signals can act in a complementary manner, and might work together with attractive signals to control cell movement and tissue location precisely.
• chemonastia or chemokinesis : random movements
• ameboid movement : the movement of an ameba or leukocyte by virtue of the flow of cytoplasm, resulting in the protrusion of a pseudopodium, or a movement similar to it.
• euglenoid movement : a wormlike writhing movement, usually nonprogressive, resulting from local expansion and contraction of the body, seen in flagellates with thin pellicles and very plastic bodies, as in certain species of the order Euglenida and certain other protozoa.
• flagellar movement by flagellum/flagella
• ciliar movemente by cilia
• slinding movement by ?
Cell migration in 3D ECM : a 5-step model of cell migration in 2D was established over the past 30 years. When cells move in 3D, such as in tissues, an additional component is the proeolytic remodelling of the ECM.
• step 1 : protrusion of the leading edge. Growing actin filaments connect to adaptor proteins and push the cell membrane in an outward direction. Actin polymerizes by coupling to the actin-nucleating ARP2/3 complex, which binds to the Wiscott-Aldrich syndrome protein (WASP), a multifunctional adaptor protein^ref. The ARP2/3/WASP complex connects to the inner leaflet of the plasma membrane via clustered phosphoinosites (PIPs) inserted therein^ref. ARP2/3 can further interact laterally with pre-exising actin filaments and induce branching of pre-existing filaments to actin networks^ref. PIPs also bind and activate guanine-nucleotide exchange factors (GEFs) that regulate the activity of the small GTPases RAC, CDC42 and RHO, as well as RAS^ref. In one pathway, CDC42 binds WASP and PIPs, which activates WASP and thereby induces filopodial ruffling and pseudopod extension^{ref1, ref2}. Chemokines and growth-factor receptors (CK-Rs, GFRs) activate phosphatidylinositol 3-kinase (PI3K) and phosphatidylinositol 4,5-kinase (PI45K), which are the key enzymes that generate PIPs^{ref1, ref2}, and further engge RAC, CDC42 and RHO^{ref1, ref2, ref3}
• step 2 : cell-matrix interaction and formation of focal contacts. Integrin come into contact with ECM ligands and cluster in the cell membrane^{ref1, ref2}. Clustered integrins recruit adaptor and signalling proteins via their intracellular domains, thereby inducing phosphorylation and dephosphorylation signals into the cell ("outside in" signalling)^{ref1, ref2}. The integrin cytoplasmic tail directly interacts with a-actinin, talin, the focal adhesion kinase (FAK), and other proteins such as tensin^{ref1, ref2, ref3, ref4}. All these proteins can bind adaptor proteins - through SH2, SH3 or proline-rich domains - to recruit actin-binding proteins (vinculin, paxillin and more a-actinin) as well as regulatory molecules (PI3K and RHO-family GTPases) to focal contacts^{ref1, ref2, ref3}. A link between the actin/ARP2/3 complex and emerging focal contacts is provided by vinculin^ref. The assembly of focal contacts is directly and indirectly induced by various signalling pathways, such as active PI3K, protein kinase C (PKC) and RHO GTPases ("inside-out" signalling)^{ref1, ref2, ref3, ref4}.
• step 3 : recruitment of surface proteases to ECM contacts and focalized proteolysis. Surface proteases become concentrated near substrate binding sites^ref. In close proximity to the cell surface, proteases cleave ECM components, such as collagen, fibronectin and laminins, as well as pro-MMPs, to create active soluble MMPs, such as MMP2^{ref1, ref2, ref3}. MT1-MMP, MMP1 and other collagenases cleave native collagens, along with other ECM macromolecules, into smaller fragments, which, in turn, are accessible to subsequent degradation by gelatinases (MMP2 and MMP9)^{ref1, ref2, ref3} or serine proteases.
• step 4 : cell contraction by actomyosin. Active myosin II binds to actin filaments (then termed actomyosin) and generates actomyosin contraction^{ref1, ref2, ref3}. The Ca²⁺- and calmodulin-dependent myosin light-chain kinase (MLCK) phosphorylates the myosin light chain (MLC), which activates myosin II. This is counteracted by dephosphorylation via the MLC phosphatase (MLCPtase)^ref. RHO regulates actomyosin contraction predominantly through its effector, ROCK, which phosphorylates and inhibits MLCPtase^{ref1, ref2}
• step 5 : detachment of the trailing edge. At the trailing edge, focal contact disassembly occurs through several mechanisms. Actin binding and severing proteins (for example, gelsolin and cofilin) cap actin filaments and cause actin filament strand breakage, respectively, thereby promoting filament turnover^ref. Phosphatases limit the assembly of cytoskeletal proteins^ref. The cytoplasmic protease calpain cleaves focal contact components (talin, cytoplasmic tail of b₁ and b₃ integrins)^{ref1, ref2}. FAK causes focal contact disassembly by yet unknown mechanisms^{ref1, ref2}. Focal contacts are further weakened through proteolytic cleavage of adhesion receptors by sheddases^ref and the accumulation of collagen fragments that are generated while the cell moves forward^ref. Following focal contact disassembly, integrins detach from the substrate and become internalized via endocytic vesicles for recycling towards the leading edge^ref or deposited onto the substrate^{ref1, ref2}.
Differences in cellular and molecular migration mechanisms :

characteristic	mesenchymal	amoeboid
cell shape	elongated, fibroblast-like (length 50-200 mm)	roundish/elliptoid (length 10-30 mm)
growth in culture	adhesive	growth in suspension
migration velocity	low (0.1-1 mm/min)	low to high (0.1-20 mm/min)
cell-matrix interactions	integrins and proteases focalize	integrins and proteases are non-focalized
structure of actin cytoskeleton	cortical and stress fibers	cortical
adhesion force generated	high, fibre pulling and bundling	low, minor fibre bending
proteolytic ECM remodelling	present to extensive	not present
cellular migration mechanism	traction dependent	propulsive, cytoplasmic streaming
mechanism overcoming matrix barriers	path generation, formation of proteolytic ECM defects	path finding, propulsion and cytoplasmic forward flow ("streaming"); squeezing through narrow regions (contriction ring)
prototypic non-neoplastic cell	fibroblast, smooth muscle cell	lymphocyte, neutrophil
neoplastic cell, carcinoma	fibrosarcoma, glioblastoma, dedifferentiated epithelial cancer	lymphoma, SCLC, small-cell prostate cancer

Web resources :
• companies offering systems and reagents to study cell migration : 3DM, Accuri Cytometers, Agilent, Andor Technology, Apogee Instruments, Applied BioPhysics, Applied Cytometry, Applied Scientific, BectonDickinson, Beckman Coulter, BioCat GmbH, Biomedical Photometrics, Bio-Rad, Cambio, Cell Biolabs Inc., Chroma Technology, Clontech, EMD Biosciences, Eppendorf, Fujifilm, Guava Technologies, Harvard Apparatus, Inbiolabs, Innovative Cell Technologies, Invitrogen, Ibidi, Kodak, La Vision Biotec, Leica Microsystems, Lightools, Micro Video Instruments, Millipore, Molecular Devices, MP Biomedicals, Nanoptek, Neuroprobe, Nikon Instruments, Olympus, Omega Optical, Perkin Elmer Life Sciences, Pierce Biotechnology, Princeton Instruments, Qimaging, Trevigen, Sigma Aldrich, Synthecon, Zeiss,
• Cell Migration Gateway by Cell Migration Consortium and Nature Publishing Group

• Michael Dean  : The Human ATP-Binding Cassette (ABC) Transporter Superfamily. Bethesda (MD): NCBI, National Library of Medicine (US); 2002 Nov. [free at NCBI BookShelf !]
• Varki, Ajit; Cummings, Richard; Esko, Jeffrey; Freeze, Hudson; Hart, Gerald; Marth, Jamey : Essentials of Glycobiology. 1^st ed.; Cold Spring Harbor Laboratory Press; c1999.
• Lipid biology in Science Vol.294, 30 November 2001

Copyright © 2001-2014 Daniele Focosi. All rights reserved  |  Terms of use  | Legal notices
About this site  |  Site map  |  Acknowledgements | Open forum  |    |  Current link partners
 Abbreviations and acronyms  |  Medical terminology  |  Add a link  |  Translate   |  Softwares

---

Copyright © 2001-2014 Daniele Focosi. All rights reserved  |  Terms of use  | Legal notices
About this site  |  Site map  |  Acknowledgements | Open forum  |    |  Current link partners
 Abbreviations and acronyms  |  Medical terminology  |  Add a link  |  Translate   |  Softwares

---