Protein structure three-dimensional

Because the number of protein three-dimensional structures completed is relatively small, much of our understanding of the metal center structures comes from studies on inorganic model compounds. Although it is beyond the scope of this chapter to discuss these compounds separately, we have integrated some of the results in our discussion of the relevant protein structures. 

The Status of Predicting Protein Three-Dimensional Structure... 

J. Moult, Predicting protein three-dimensional structure, Curr. Opin. Biotechnol. 1999, 10, 583-588. 

Large-scale sequencing projects produce data of genes hence they produce protein sequences at an amazing pace. Although experimental determination of protein three-dimensional structure has become more efficient, the gap between the number of known sequences and the number of known structures is rapidly... 

Gowri VS, Pandit SB, Karthik PS et al (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res 31 486-488... 

Various schemes have been developed for the classification of protein three-dimensional structures. One common scheme is the classification based on the four tertiary super classes, namely, all a (proteins having mainly a-helix secondary structure), all P (mainly P-sheet secondary structure), a+p (segment of a-helices followed by segment of P-sheets), and o/p (alternating or mixed a-helix and P-sheet segments) (Levitt, 1976). A fifth class is often added to account for globular proteins with irregular secondary... 

Furthermore, the parameters derived from protein three-dimensional structures characterize the topology of proteins, which play an important role in kinetics of protein folding. 

Recently, Lindorff-Larsen el al.uo included the order parameter (S 2) in the target function, and refined an ubiquitin X-ray structure by restrained molecular dynamics (Section 6.4) to obtain an NMR structure ensemble (Section 6.5) from the trajectories. They simulated the values of RDCs (Section 9.1) and side chain scalar coupling from the calculated ensemble to confirm that the method can determine the protein three-dimensional structure and dynamic structure simultaneously. The simulated values were in good agreement with the corresponding measurement data. The simulation accuracy was improved from the preliminary calculated structure without the order parameters. The approach is typically important, because they tried to link the ensemble with a dynamic structure directly. 

J. Moult. Predicting protein three-dimensional structure. 

Sowdhamini, R., et al., Protein three-dimensional structural databases domains, structurally aligned homologues and superfamilies. Acta Crystallogr D Biol Crystallogr, 1998. 

The electrostatic bond strength depends strongly on the value assumed for the dielectric constant, and therefore on the separation of the charges and the proximity of any water molecules. One reason why the theoretical prediction of protein three-dimensional structure from the amino acid sequence is so difficult is because of the prevalence of water in vivo and the large value of the dielectric constant for water (80) as a result the force between charges varies dramatically depending on the number of water molecules interposed between the charges. 

Fig. 16J. The relationship between the percentage sequence differences and the rms distance differences between topologically equivalent C positions in optimally superposed pairs of homologous protein three-dimensional structures (taken from [2]). The are for all equivalent amino acids and the + are for those whose side chains contribute to the solvent inaccessible core. The lines in a are the best unweighted least-squares fits of quadratic equations for the following sets of points TA is for all points TI is for all + points BA and BI are for P sheet proteins while AA and AI are for those with a helices, b shows data for P sheet proteins and c for a helical proteins. Lines linking and + points for individual proteins are plotted in b and c...

Proteins are essential structural and functional components of all living organisms. These macromolecules, with molecular weights above 10000, consist of clearly defined chains (or sequences) of amino acids linked by peptide bonds (Section 5.2.3). According to pH, proteins may be positively or negatively charged. They may also be at the isoelectric point (Section 9.2.4) and, therefore, neutral. The sequence of amino acids in the polypeptide chains determines proteins three-dimensional structures, i.e. their spatial configurations. 

Hierarchical Classification of Protein Three-Dimensional Structures. 

Ion-exchange chromatography has been used in the separation of ionic species for more than half a century. Early separations were achieved with either sulfonated or quatemized polystyrenedivinylbenzene (PSDVB). Unfortunately, these materials are often unsuitable for protein separations because the strong nonspecific adsorption between the hydrophobic sorbents and proteins necessitates the use of organic solvent or extremes in pH to achieve elution. Such conditions are sufficiently harsh to denature protein three-dimensional structure and, consequently, alter biological activity. 

The basic thesis has served as the stimulus for a large number of studies directed towards the prediction of protein three-dimensional structures from their amino-acid sequences alone. Implicit in most of the predictive methods investigated are two concepts (i) that there is in the protein the clearly-observed hierarchical structural arrangement (primary structure - secondary structure - secondary aggregates or super-secondary structure - domains - total structure) which has already been discussed in the previous section and (ii) that the folding process of a random chain to give the stable native structure is kinetically-controlled and that it proceeds via a characteristic and predictable pathway. This pathway is visualized as requiring nucleation at various sites around which the subsequent... 

R 630 T. Kohno, High Throughput NMR Analyses of Protein Three-Dimensional Structures , Seikagaku, 2004,76,1443... 

Enzyme deactivation may also result from chemical modifications which alter the protein three-dimensional structure or which destroy the catalytic center. The destruction of the active site may result from an alteration of the reactive moieties or from a change in the local conformation. 

---