Proteins structure and conformation

Jorgensen, P.L. (1982). Mechanism of the Na/K pump. Protein structure and conformations of the pure Na/K ATPase. Biochim. Biophys. Acta 694, 27-68. 

Danielson MA, Falke JJ (1996) Use of F-19 NMR to probe protein structure and conformational changes. Annu Rev Biophys Biomol Struct 25 163-195... 

Abstract Conjugated polymers have many unique photophysical properties that make them useful for a variety of applications within the fields of chemistry, molecular biology, and medicine, specifically their ability to produce a conformation-dependant spectral signature reflective of changes in their local environment. This physical property makes conjugated polymers an indispensible tool in the toolbox of fluorescent reporters, and within this chapter, their utilization as molecular probes for studying protein structure and conformation is emphasized. 

X-ray crystallography and NMR spectroscopy are both powerful tools for the investigation of protein structure and conformation. Vital information may be obtained about the binding sites and catalytic sites of enzymes, particularly if the enzyme can be crystallized with the natural substrate or some smaller, analogue molecule in place at the active site. It occurred to us that our epoxyalkyl glycosides, suitably modified to contain either an iodine (heavy) or fluorine (magnetically active) atom, would be ideal molecules to assist in X-ray crystallographic and NMR analyses, respectively. 

At this juncture, it is useful to discuss the experimental methods that are of value in studying and separating the various kinds of interactions in macromolecular systems. A variety of experimental methods have been applied to the determination of protein structure and conformation in solution, and these have been summarized by Kauzmann (1959). In the discussion which follows, emphasis is placed on those methods which have so far been of most use in studies of proteins in nonaqueous solvents, and these remarks should be considered as supplementary to the Kauzmann summary. 

EE Cohen, ID Kuntz. Tertiary stiaicture prediction. In CD Easman, ed. Prediction of Protein Structure and the Principles of Protein Conformation. New York Plenum Press, 1989, pp 647-705. 

A prior distribution for sequence profiles can be derived from mixtures of Dirichlet distributions [16,51-54]. The idea is simple Each position in a multiple alignment represents one of a limited number of possible distributions that reflect the important physical forces that determine protein structure and function. In certain core positions, we expect to get a distribution restricted to Val, He, Met, and Leu. Other core positions may include these amino acids plus the large hydrophobic aromatic amino acids Phe and Trp. There will also be positions that are completely conserved, including catalytic residues (often Lys, GIu, Asp, Arg, Ser, and other polar amino acids) and Gly and Pro residues that are important in achieving certain backbone conformations in coil regions. Cys residues that form disulfide bonds or coordinate metal ions are also usually well conserved. 

Fasman G (1989) Prediction of protein structure and the principles of protein conformation. Plenum Press, New York... 

Transition from the high-energy phosphoform E]P[3Na] to the K-sensitive E2P[2Na] of Na,K-ATPase are accompanied by conformational transitions in protein structure and changes of the capacity and orientation of cation sites. In the Ej form of Na,K-ATPase, the exposure of Chys (Leu ) and Trys (Arg ) to cleavage reflects that the cation sites of the phosphoprotein are in a conformation oriented towards the cytoplasm with a capacity for occlusion of three Na ions. The E2 form... 

One of the most characteristic features of FRET is its sensitive dependency on the fluorophore distance. This is advantageously used to evaluate structures and conformational changes of peptides, glycopeptides, and proteins among other molecules [164-166], The conformational change of the lipopeptide antibiotic daptomycin from an inactive linear form to a biological active cyclic form... 

Dicko, C., Knight, D., Kenney, J. M., and Vollrath, F. (2004b). Secondary structures and conformational changes in flagelliform, cylindrical, major, and minor ampullate silk proteins. Temperature and concentration effects. Biomacromolecules 5, 2105-2115. 

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