Proteins and Proteomics

Proteins are complex, macromolecules comprised of amino acids linked by peptide bonds into long chains. The sequence (primary structure) and properties of constituent amino acids generate the 3D conformational structure (tertiary and quaternary structure) that is vital to the biological function of proteins. (click to enlarge image)


Proteins are essential to the structure and biological viability of all living cells and viruses. The cellular proteome is the total cellular protein under a particular set of conditions, while the complete proteome is the sum of all potential proteomes of a cell. Proteomics has become the subject of much research in cell and molecular biology.

Proteins play a number of vital roles as:
a. Enzymes or subunits of enzymes – catalyzing cellular reactions.
b. Structural or mechanical roles – structural components of tissues, components of the cytoskeleton, centrioles, cilia and flagella, microtubules, molecular motors.
c. Intracellular and intercellular signaling functions – ion channels, receptors, membrane pumps.
d. Regulatory proteins or adaptor proteins in genetic transcription, RNA processing, spliceosomes.
e. Products of immune and inflammatory responses that aid in targetting of foreign substances and organisms.
f. Storage and transport of various ligands.
g. The source of essential amino acids.

Almost all natural proteins are encoded by DNA, which is transcribed and processed to yield mRNA, which then serves as a template for translation by ribosomes on the rough endoplasmic reticulum.

Protein roles:
● cytoskeletal protein, enzymes, ion channels, latent gene regulatory proteins, receptor proteins, 'signaling' enzymes, signaling proteins, transcription factors
● activator,
● adaptor protein, amplifier protein, anchoring protein, bifurcation protein, coincidence detector protein, effector protein, messenger protein, modulator protein, relay protein, scaffold protein, transducer protein

Specific proteins/types : § adaptor protein : cAMP receptor binding protein § CARD domains : cofactor § collagen : core histones H2A, H2B, H3, and H4 : CRE-binding protein CREB § C-reactive protein § CRP § domains : elongation factor EF § granulysin : helicases : Helicase II : heterochromatin : histone : HP1 § immunoglobulin isotypes : inducible transcription factors : LexA repressor : mCAT2 receptor : motor proteins § NF-κB : nucleosome : PcG proteins : PCNA § (pentraxins, CRP) § PH family : Polycomb group : proteome : RecA : regulatory proteins : repressor proteins : ribosomes : RPA : serine rich (SR) splicing factors : silencers : Ski7p : small nuclear ribonucleoproteins (snRNPs) : spliceosome : SR (serine rich) splicing factors : trans-acting factors : trithorax group (trxG) : UPF1 UPF2 : upstream transcription factors :

Enzymes ♦ Enzymes : ♦ activation-induced (cytidine) deaminase ♦ adenylate cyclases ♦ AID ♦ Akt : AP endonuclease (Ape1) ♦ ATPases ♦ bonds ♦ cAMP-dependent protein kinase ♦ cyclin-dependent kinases : DNA glycosylase : DNA Ligase I : DNA polymerases : DNA polymerase I : DNA polymerase beta : DNase IV ♦ energetics : exonuclease 1 : exosome : Fen1 : Flap Endonuclease FEN-1 ♦ Fyn : general transcription factors ♦ GTPases : hOGG1 : hOGG1 oxoG repair : LigIII : MAP kinase ♦ MAPKs ♦ MEK ♦ MPF : Msh2-Msh3 ♦ mTOR : MutS, MutL, and MutH : 8-oxoguanine glycosylase : oxoG repair hOGG1 : PCNA ♦ PDK1 ♦ PTEN ♦ PDK1 ♦ phosphatases ♦ phospholipases ♦ phosphodiesterases ♦ phosphorylases ♦ PIKK ♦ PI3K ♦ PKA ♦ PKB ♦ PKCs ♦ protein kinases ♦ reaction energetics ♦ receptor tyrosine kinases : RNA polymerase: Replication factor C : reverse transcriptase : ribozymes : RNA polymerase II ♦ serine/threonine kinases : spliceosomal-mediated RNA trans-splicing SMaRT : trans-splicing ribozymes ♦ UNG2 ♦ uracil-DNA glycosylase : UvrD : XRCC1 :

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tags [Proteins] [Proteomics]

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fibronectin

Fibronectin (FN) is a high molecular weight, multidomain glycoprotein, comprising about 5% by weight of carbohydrate.

Fibronectin exhibits diverse recognition functions located on distinct fragments or domains, so FN can interact with a variety of macromolecules including/on :
● cytoskeleton
● extracellular matrix – collagen, glycosaminoglycans, proteoglycans, tenascin, fibulin and thrombospondin
● circulating coagulation factors – Fn is covalently incorporated into fibrin clots through the transglutaminase action of coagulation factor XIII, improving fibroblast adhesion
● fibrinolytic system
● acute phase proteins
● complement system
● cell-surface receptors on a variety of cells including fibroblasts, neurons, phagocytes and bacteria – integrins (through RGD tripeptide)
● itself, forming fibrillar entities
● small molecules such as gangliosides, sugars, and Ca ions.

Fibronectin (FN) participates in tissue repair, embryogenesis, blood clotting, and cell migration/adhesion. Cells of most tissues synthesize fibronectin. Soluble fibronectin is produced by hepatocytes and circulates, in its disulfide-bonded dimeric form, in the plasma. The soluble protomer is a compact, flexible dimer that can be converted into an insoluble, fibrillar network. The soluble-to-fibrillar conversion is a highly regulated process involving integrins and possibly other cell-surface receptors [ref] including uPAR (urokinase-type plasminogen activator receptor) [ref] and a cell-surface proteoglycan [ref].[s]

The insoluble fibronectin dimer is synthesized by fibroblasts, chondrocytes, endothelial cells, macrophages, as well as certain epithelial cells. Electron microscopic analyses of natural thin fibrils (5-18nm diameter), made by fibroblasts in culture, clearly indicate an ordered arrangement and suggest a model in which extended protomers (130nm long) are arranged end-to-end with an overlap of about 14 nm [ref]. As an extracellular adhesion molecule, FN binds to integrins and participates in wound healing.

Cell-surface receptors or fibrinogen, collagen and fibrin (as extracellular matrix proteins) facilitate the adherence of microorganisms to host tissues [ref]. The Hep-2 domain of fibronectin interacts with envelope glycoproteins on some retroviruses. Fibronectin is able to bind both the virus and cell-surface receptors, concentrating viruses on the surface of the cells, enhancing viral uptake by cells.

The structural isoforms of fibronectin arise from alternative splicing of a single gene, and possess a variable region plus three types of repeated internal regions (homologous, repeating modules I, II and III) +/- disulfide bonds.

[more] [] The Type I module of fibronectin [] The Type II module (F2) [] segment of fibronectin , four Type III modules []

tags [Proteins] [fibronectin]

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