Protein small proteins

However, analysis of protein mixtures derived from cells, tissues, and body fluids by 2D PAGE by no means represents a comprehensive picture of the proteins in the mixture. Proteins with extreme isoelectric points, large proteins, small proteins, and hydrophobic proteins are commonly not amenable to 2D PAGE and hence can be easily missed. Furthermore, low abundant proteins are often not detected in 2D gels when proteins of high abundance are present. This limitation is particularly relevant when analyzing serum or other body fluids, where protein amounts vary by ten orders of magnitude (Anderson and Anderson 1998). 

Polypeptides with more than a few hundred amino acid residues often fold into two or more stable, globular units called domains. In many cases, a domain from a large protein will retain its correct three-dimensional structure even when it is separated (for example, by proteolytic cleavage) from the remainder of the polypeptide chain. A protein with multiple domains may appear to have a distinct globular lobe for each domain (Fig. 4-19), but, more commonly, extensive contacts between domains make individual domains hard to discern. Different domains often have distinct functions, such as the binding of small molecules or interaction with other proteins. Small proteins usually have only one domain (the domain is the protein). 

Most transporters are proteins. Small proteins can bind some substance on one side of a membrane, diffuse across the membrane, and then release that substance on the other side. Such mobile carriers may bind a single substance, or they may bind two different substances, like the proton-solute symporter portrayed in Figure 3-l4a. Candidates for transport by a proton symporter in plants include inorganic ions such as Cl- and metabolites such as sugars and amino acids. Many substances apparently move in pores or channels, which can be membrane-spanning proteins. Some channels can have a series of binding sites, where the molecule or molecules transported go from site to site through the membrane (Fig. 3-l4b). As another... 

As in signaling by cytokine receptors, phosphotyroslne residues in activated RTKs serve as docking sites for proteins involved in downstream signal transduction. Many phos-photyrosine residues in activated RTKs interact with adapter proteins, small proteins that contain SH2, PTB, or SH3 domains but have no intrinsic enzymatic or signaling activities (see Figure 14-6). These proteins couple activated RTKs to other components of signal-transduction pathways such as the one involving Ras activation. 

Fluorescein-labeled proteins are obtained by reacting proteins with FITC (see Fig. 3). Dissolve the protein (small proteins 0.1-0.3 mg, large proteins or antibodies 0.1-1 mg)in 100 pi of 0.1 M sodium phosphate buffer (pH 8.0). If protein activity is decreased by phosphate ions, the labeling reaction can be carried out in 0.1 M bicarbonate, HEPES, or borate buffers at the same pH. However, do not use buffers containing free amino groups such as Tris or glycine these buffers will react with FITC. 

At the top of the SCOP hierarchy are 11 different classes alpha, beta, alpha and beta (a/p), alpha plus beta (a + p), multidomain proteins, membrane and cell-surface proteins, small proteins, coiled coil proteins, low-resolution protein structures, peptides, and designed proteins. Note that only the first seven classes are true classes. The remaining ones serve as place holders for protein domains that cannot (yet) be classified among the major classes and are maintained in SCOP for the sake of completeness and compatibility with the PDB. 

Equilibrium constants for protein-small molecule association usually are easily measured with good accuracy it is normal for standard free energies to be known to within 0.5 kcal/mol. Standard conditions define temperature, pressure and unit concentration of each of the three reacting species. It is to be expected that the standard free energy difference depends on temperature, pressure and solvent composition AA°a also depends on an arbitrary choice of standard unit concentrations. 

Ortiz A R, A Kolinski and J Skolnick 1998. Fold Assembly of Small Proteins Using Monte C Simulations Driven by Restraints Derived from Multiple Sequence Alignments. Jourru Molecular Biology 277 419-446. 

Eleven chirality centers may seem like a lot but it is nowhere close to a world record It is a modest number when compared with the more than 100 chirality centers typ ical for most small proteins and the thousands of chirality centers present m nucleic acids A molecule that contains both chirality centers and double bonds has additional opportunities for stereoisomerism For example the configuration of the chirality center m 3 penten 2 ol may be either R or S and the double bond may be either E or Z There fore 3 penten 2 ol has four stereoisomers even though it has only one chirality center... 

Fig. 5. Protein folding. The unfolded polypeptide chain coUapses and assembles to form simple stmctural motifs such as -sheets and a-hehces by nucleation-condensation mechanisms involving the formation of hydrogen bonds and van der Waal s interactions. Small proteins (eg, chymotrypsin inhibitor 2) attain their final (tertiary) stmcture in this way. Larger proteins and multiple protein assembhes aggregate by recognition and docking of multiple domains (eg, -barrels, a-helix bundles), often displaying positive cooperativity. Many noncovalent interactions, including hydrogen bonding, van der Waal s and electrostatic interactions, and the hydrophobic effect are exploited to create the final, compact protein assembly. Further stmctural...

Molecular Interactions. Various polysaccharides readily associate with other substances, including bile acids and cholesterol, proteins, small organic molecules, inorganic salts, and ions. Anionic polysaccharides form salts and chelate complexes with cations some neutral polysaccharides form complexes with inorganic salts and some interactions are stmcture specific. Starch amylose and the linear branches of amylopectin form inclusion complexes with several classes of polar molecules, including fatty acids, glycerides, alcohols, esters, ketones, and iodine/iodide. The absorbed molecule occupies the cavity of the amylose helix, which has the capacity to expand somewhat to accommodate larger molecules. The starch—Hpid complex is important in food systems. Whether similar inclusion complexes can form with any of the dietary fiber components is not known. 

Polypeptides. These are a string of a-amino acids usually with the natural 5(L) [L-cysteine is an exception and has the R absolute configuration] or sometimes "unnatural" 7f(D) configuration at the a-carbon atom. They generally have less than -100 amino acid residues. They can be naturally occurring or, because of their small size, can be synthesised chemically from the desired amino acids. Their properties can be very similar to those of small proteins. Many are commercially available, can be custom made commercially or locally with a peptide synthesiser. They are purified by HPLC and can be used without further purification. Their purity can be checked as described under proteins. 

With mostly unambiguous data, this protocol has been successfully used for proteins with up to 160 residues [62]. Although virtually all structures converge to the correct fold for small proteins, we observe that approximately one-third of the structures are misfolded for larger proteins, or for low data density, or many ambiguities (see, e.g.. Ref. 63). We have also used this protocol for most structure calculations with the automated NOE assignment method ARIA discussed in the next section. 

Standard calculation methods developed for small proteins are sufficiently powerful to solve protein structures and complexes in the 30 kDa range and beyond [97,98] and protein-nucleic acid complexes [99]. Torsion angle dynamics offers increased conver-... 

Although comparative modeling is the most accurate modeling approach, it is limited by its absolute need for a related template structure. For more than half of the proteins and two-thirds of domains, a suitable template structure cannot be detected or is not yet known [9,11]. In those cases where no useful template is available, the ab initio methods are the only alternative. These methods are currently limited to small proteins and at best result only in coarse models with an RMSD error for the atoms that is greater than 4 A. However, one of the most impressive recent improvements in the field of protein structure modeling has occurred in ab initio prediction [155-157]. 

AR Ortiz, A Kolinski, J Skolnick. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J Mol Biol 277 419-448, 1998. 

T Dandekar, P Argos. Folding the mam chain of small proteins with the genetic algorithm. J Mol Biol 236 844-861, 1994. 

Figure 2.19 Organization of polypeptide chains into domains. Small protein molecules like the epidermal growth factor, EGF, comprise only one domain. Others, like the serine proteinase chymotrypsin, are arranged in two domains that are required to form a functional unit (see Chapter 11). Many of the proteins that are involved in blood coagulation and fibrinolysis, such as urokinase, factor IX, and plasminogen, have long polypeptide chains that comprise different combinations of domains homologous to EGF and serine proteinases and, in addition, calcium-binding domains and Kringle domains.

Small protein modules form adaptors for a signaling network... 

To obtain the secondary and tertiary stmcture, which requires detailed information about the arrangement of atoms within a protein, the main method so far has been x-ray crystallography. In recent years NMR methods have been developed to obtain three-dimensional models of small protein molecules, and NMR is becoming increasingly useful as it is further developed. 

Figure 18.11 Electron-density maps at different resolution show more detail at higher resolution, (a) At low resolution (5.0 A) individual groups of atoms are not resolved, and only the rodlike feature of an

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