Pathway determination, protein folding

In this introductory chapter, the fundamental questions at the molecular level focus on two points. The first point is a discussion of the thermodynamic and kinetic determination of protein folding. In fact, it can be divided in two related questions. Does the native protein correspond to the most stable conformation Does the native protein corresponds to a unique structure The second point is related to the pathway of protein folding, the existence, the number, and the nature of the intermediates. In this presentation of the fundamental questions, we will try to delineate what decisive arguments, if any, could be presented, and what significant experiments could be made to prove or disprove the different hypotheses. 

Nevertheless, conformational computations have produced important pieces of information. They have indicated the importance of the different energy contributions in determining protein folding. If they have not proposed a definite pathway of protein folding, they have at least suggested some plausible steps. In fact, different models are proposed in computations and nothing for the moment allows one to make a decision between them. 

Determination of Kinetic Pathway of Protein Folding and Unfolding Using Disulfide Bonds as Conformational Probe... 

The term "structural genomics" is used to describe how the primary sequence of amino acids in a protein relates to the function of that protein. Currently, the core of structural genomics is protein structure determination, primarily by X-ray crystallography, and the design of computer programs to predict protein fold structures for new proteins based on their amino acid sequences and structural principles derived from those proteins whose 3-dimensional structures have been determined. Plant natural product pathways are a unique source of information for the structural biologist in view of the almost endless catalytic diversity encountered in the various pathway enzymes, but based on a finite number of reaction types. Plants are combinatorial chemists par excellence, and understanding the principles that relate enzyme structure to function will open up unlimited possibilities for the... 

No attempt to determine the folding pathway of a protein from the denatured to the native state either by energy minimization or by molecular dynamics has yet been successful. Many people believe that it would be more effective to approach the problem through a study of the formation and interaction of secondary structural units. A conservative appraisal of the situation is that this problem is not one that can be solved by increase in computer power alone. 

T. E., Protein-folding pathways determined nsing disulphide bonds. Bioessays 14, 195-199, 1992 Day, R. and Daggett, V, All-atom simnlations of protein folding and unfolding, Adv. Protein Chem. 66, 373 03, 2003. 

For a mechanistic understanding of protein folding, it is necessary to determine the sequence of intermediate states between the fully unfolded and fully folded forms of a polypeptide chain (i.e. the folding pathway) and to describe the major intermediates in structural and kinetic terms. One of the... 

J. D. Bryngelson, J. N. Onuchic, N. D. Socci et al. Funnels, pathways, and the energy landscape of protein-folding - a synthesis. Proteins, 21 (1995), 167 D. K. Klimov and D. Thirumalai. Criterion that determines the foldability of proteins. Physical Review Letters, 76 (1996), 4070 H. S. Chan and K. A. Dill. Protein folding in the landscape perspective chevron plots and non-arrhenius kinetics. Proteins, 30 (1998), 2. 

The disulfide formation depends on the protein conformation that places Cys residues into appropriate proximity and the disulfide redox potential that determines the intrinsic stability of protein disulfide bonds. For catalytic activity, the reduced dithiol form of protein disulfide isomerase is required. Protein disulfide isomerase is a folding catalyst that assists protein folding (Gilbert, 1997). The enzyme increases the rate of the overall folding process of the substrate protein without altering its pathway. 

In order to determine the folding pathway, it is important to examine multiple positions in a protein. This has... 

The major conformational changes in disulfide bonded proteins, such as BPTl and ribonuclease A [88], can be understood in terms of disulfide bond rearrangement. Thus, the conformations of the intermediates that determine the folding pathways are specified in terms of the S-S bonds. In such proteins the S-S bonds serve as a surrogate reaction coordinate. These observations enable us to develop the proximity rule based on the following general principles. 

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