Proteins structure-function relationships

Bode W, Turk D, Karshikov A. The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci. 1992 1 426-471. 

Chemical approaches are invaluable means for the preparation of homogeneous lipidated proteins on a scale which permits X-ray crystal structure determination and many other biophysical studies. Moreover, chemical synthesis allows for manipulation of the protein structure and incorporation of difference functional groups into proteins. These strategies make it possible to investigate structure-function relationships, protein-protein interactions, protein-membrane interactions, intracellular localization and function of lipidated proteins in vitro and in cells. A combination of chemistry and biology has allowed the study of biological functions previously not possible through traditional biochemical approaches. 

Bradshaw, R.A., Murry-Rust, J., Ibanez, C.F., McDonald, N.Q., Lapatto, R., and Blundell, T.L., 1994, Nerve growth factor structure/function relationships. Protein Sci., 3 1901-1913. 

Structure—function relationships of prolactin among a variety of species have been pubUshed (17,18). Only one gene for prolactin appears to exist (19). Although classically placed in the category of simple protein hormones, prolactin can be glycosylated. Carbohydrate attachment occurs at Asn-31, where the consensus glycosylation sequence Asn—X—Ser is found. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

The aim of the second dimension depth is to consider protein 3D-stmctures to uncover structure-function relationships. Starting from the protein sequences, the steps in the depth dimension are structure prediction, homology modeling of protein structures, and the simulation of protein-protein interactions and ligand-complexes. 

In general the relevance of predictions of structure-function relationships based on molecular modeling and structural bioinformatics are threefold. First they can be used to answer the question of which partners (proteins) could interact. Second, predictions generate new hypotheses about binding site, about molecular mechanisms of activation and interaction between two partners, and can lead to new ideas for pharmacological intervention. The third aim is to use the predictions for structure-based drug design. 

Scientists initially approached structure-function relationships in proteins by separating them into classes based upon properties such as solubility, shape, or the presence of nonprotein groups. For example, the proteins that can be extracted from cells using solutions at physiologic pH and ionic strength are classified as soluble. Extraction of integral membrane proteins requires dissolution of the membrane with detergents. 

Historically the Shaker (Sh) K channel was the first K channel which was cloned and characterized [6-10]. Subsequently many more channel cDNAs and genes have been isolated and studied. Yet Sh channels remained in the forefront of channel research. The study of Sh channel mutants has provided the most thorough insight into structure-function relationships of K channels to date. I will first discuss in this chapter the primary sequences of voltage-gated channels. I will only use a few selected examples for discussion. As of this time, so many related K channel protein sequences have been published that it is not feasible to discuss all of them. Subsequently, I will describe in detail the present knowledge about functional K" " channel domains which are implicated in activation, inactivation and selectivity of the channel. 

It is clearly impossible to give a comprehensive overview of this rapidly expanding field. I have chosen a few experts in their field to discuss one (class of) transport protein(s) in detail. In the first five chapters pumps involved in primary active transport are discussed. These proteins use direct chemical energy, mostly ATP, to drive transport. The next three chapters describe carriers which either transport metabolites passively or by secondary active transport. In the last three chapters channels are described which allow selective passive transport of particular ions. The progress in the latter field would be unthinkable without the development of the patch clamp technique. The combination of this technique with molecular biological approaches has yielded very detailed information of the structure-function relationship of these channels. 

Farrell, H. M., Jr., Qi, P. X., and Uversky, V. N. (2006b). New views of protein structure Implication for potential new protein structure-function relationships. In "Advances in Biopolymers Molecules, Clusters, Networks and Interactions", (M. L. Fishman, P. X. Qi, and L. Wicker, Eds), pp. 1-18. American Chemical Society, Washington, DC. 

Fukuoka was found to be homozygous for the 1615 G to A (539 Asp to Asn) mutation. This mutation occurred at relatively conserved amino acid residues and caused an alteration in hydrophobicity. Recently, we examined the structure-function relationship of these variants using the recombinant protein (F14). Although all of the four variants were found to be heat labile, the residual GPI activity seems to reflect clinical severity, such as the degree of anemia and episodes of hemolytic crisis. GPI Matsumoto, associated with severe anemia and hemolytic crisis, was extremely unstable, and GPI Iwate, which is associated with compensated hemolytic anemia, showed moderate heat instability. Affinity for substrate, fructose-6-phosphate, was slightly decreased in GPI Narita and GPI Fukuoka, which were associated with moderate anemia and hemolytic crisis. 

Savarese TM, Fraser CM. In vitro mutagenesis and the search for structure-function relationships among G protein-coupled receptors. Biochem J 1992 283 1-19. 

Cubitt, A. B., Woollenweber, L. A. and Heim, R. (1999). Understanding structure-function relationships in the Aequorea victoria green fluorescent protein. Methods Cell. Biol. 58, 19-30. 

Because of the structure-function relationship for (globular) proteins, adsorption-induced changes in the molecular structure are likely to affect the biological activity of the protein, e.g., the enzymatic activity. In soils, as well as in a wide variety of other systems, the impact on biological... 

The cloning, sequencing and expression of several transporter proteins, including that for 5-HT, has aided considerably in understanding structure/function relationships of transporter proteins [12]. The cDNA for the SERT isolated from rat brain predicts a protein containing... 

Extensive biochemical and spectroscopic studies have been undertaken on hCP in order to investigate the nature of the copper centers and their role in structure-function relationships. However, the protein is very susceptible to aggregation, proteolysis, loss of copper, and other chemical degradations and requires careful preparation and handling in these circumstances it is difficult to review all the literature objectively and comprehensively. A three-dimensional crystal structure of hCP has been reported at a nominal resolution of 3.1A [7], but this resolution has been extended to just beyond 3.0 A. This chapter will summarize some of the more important biochemical and spectroscopic studies of the protein. It will then focus on the structural results recently obtained by X-ray crystallographic methods and attempt to explain putative functions of the protein in terms of its molecular structure. 

Comparisons between the protein and the analogs to reveal new structure-function relationships. 

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