How many conformations can proteins have

If the conformation is altered too drastically, the protein molecule may lose function -- it breaks -- it becomes denatured. Some proteins have more stable conformations if they are stabilized by disulfide bonds.

Click Here for an excellent review of the importance and function of proteins. Proteins or polypeptides are polymers of amino acids. Each different amino acid has a unique R-group which gives each amino acid an unique chemistry. The amino acids are covalently linked to each other via peptide bonds. Once polymerized, the R-groups of the various amino acids interact with each other. This then causes the polypeptide to assume a shape or conformation. Review Proteins are made of amino acids.

With this method, solid crystals of purified protein are placed in an X-ray beam, and the pattern of deflected X rays is used to predict the positions of the thousands of atoms within the protein crystal. In theory, once their constituent amino acids are strung together, proteins attain their final shapes without any energy input.

In reality, however, the cytoplasm is a crowded place, filled with many other macromolecules capable of interacting with a partially folded protein. Inappropriate associations with nearby proteins can interfere with proper folding and cause large aggregates of proteins to form in cells.

Cells therefore rely on so-called chaperone proteins to prevent these inappropriate associations with unintended folding partners. Chaperone proteins surround a protein during the folding process, sequestering the protein until folding is complete. For example, in bacteria, multiple molecules of the chaperone GroEL form a hollow chamber around proteins that are in the process of folding. Molecules of a second chaperone, GroES, then form a lid over the chamber.

Eukaryotes use different families of chaperone proteins, although they function in similar ways. Chaperone proteins are abundant in cells.

These chaperones use energy from ATP to bind and release polypeptides as they go through the folding process. Chaperones also assist in the refolding of proteins in cells. Folded proteins are actually fragile structures, which can easily denature, or unfold. Although many thousands of bonds hold proteins together, most of the bonds are noncovalent and fairly weak. Even under normal circumstances, a portion of all cellular proteins are unfolded.

Increasing body temperature by only a few degrees can significantly increase the rate of unfolding. When this happens, repairing existing proteins using chaperones is much more efficient than synthesizing new ones. Interestingly, cells synthesize additional chaperone proteins in response to "heat shock.

All proteins bind to other molecules in order to complete their tasks, and the precise function of a protein depends on the way its exposed surfaces interact with those molecules. Proteins with related shapes tend to interact with certain molecules in similar ways, and these proteins are therefore considered a protein family.

The proteins within a particular family tend to perform similar functions within the cell. Proteins from the same family also often have long stretches of similar amino acid sequences within their primary structure. These stretches have been conserved through evolution and are vital to the catalytic function of the protein. For example, cell receptor proteins contain different amino acid sequences at their binding sites, which receive chemical signals from outside the cell, but they are more similar in amino acid sequences that interact with common intracellular signaling proteins.

Protein families may have many members, and they likely evolved from ancient gene duplications. These duplications led to modifications of protein functions and expanded the functional repertoire of organisms over time. This page appears in the following eBook.

Aa Aa Aa. Protein Structure. What Are Proteins Made Of? Figure 1: The relationship between amino acid side chains and protein conformation. The defining feature of an amino acid is its side chain at top, blue circle; below, all colored circles. Figure 2: The structure of the protein bacteriorhodopsin. Bacteriorhodopsin is a membrane protein in bacteria that acts as a proton pump. What Are Protein Families? Proteins are built as chains of amino acids, which then fold into unique three-dimensional shapes.

Antibodies that bind to antigen with high affinity and hence high specificity more likely bind through a lock and key fit. Pauling, however, didn't know that the genes that encode the proteins chains in antibodies are differentially spliced and subjected to enhanced mutational rates which allow the generation of incredible antibody diversity from a limited set of genes.

Regions of disorder are enriched in polar and charged side chains which follows since these might expected to assume many available conformations in aqueous solutions compared to sequences enriched in hydrophobic side chains, which would probably collapse into a compact core stabilized by the hydrophobic effect. Mutations in the disordered regions tend to preserve the disordered region, suggesting that the disordered region is advantageous for "future" function.

In addition, mutations that cause a noncoding sequence to produce a coding one invariably produce disordered protein sequences. Disordered proteins tend to have regulatory properties and bind multiple ligands, in comparison to ordered one, which are involved in highly specific ligand binding necessary for catalysis and transport. The intracellular concentration of disordered proteins has also been shown to be lower than ordered proteins, possibly to prevent occurrences of inappropriate binding interactions mediated through hydrophobic interactions, for example.

Processes to accomplish this include more rapid mRNA and protein degradation and slower translation of mRNA for disordered proteins. For a similar reason, misfolded proteins are targeted for degradation as well. Figure A below shows the mean net charge vs the mean hydrophobicity for folded and 91 natively unfolded proteins.

Figure B shows the relative amino acid composition of globular ordered proteins compared to regions of disorder greater than 10 amino acids in disordered proteins. The two different grey bars were obtained with two different versions of the software used to analyze the proteins. Again the graph shows an enrichment of hydrophilic amino acids in disordered proteins.

Many experimental methods can be used to detect disordered regions in proteins. Such regions are not resolved well in X-Ray crystal structures have high B factors. NMR solution structures would show multiple, and differing conformations. CD spectroscopy likewise would show ill-defined secondary structure. In addition solution measurements of size light scattering, centrifugation would show larger size distributions for a given protein.

What types of proteins contain disorder? The above experimental and new computational methods have been developed to classify proteins as to their degree of disorder.

There appears to be more IDPs in eukaryotes than in archea and prokaryotes. Many IDPS are involved in cell signaling processes when external molecules signal cells to respond by proliferating, differentiating, dying, etc.