Biomedical subjects

D N Ivankov

Publications and source records attributed to D N Ivankov.

4 recordsLinked to original sources

PubMed2001

Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition.

This paper presents a new method for calculating the folding-unfolding rates of globular proteins. The method is based on solution of kinetic equations for a network of folding-unfolding pathways of the proteins. The rates are calculated in the point of thermodynamic equilibrium between the native and completely unfolded states. The method has been applied to all the proteins listed by Jackson [Jackson, S. E. (1998) Folding Des. 3, R81-R91] and some peptides. Although the studied protein chains differ by more than 1 order of magnitude in size and exhibit two- as well as three-state kinetics in water, and their folding rates cover more than 11 orders of magnitude, the theoretical estimates are reasonable close to the experimentally measured folding rates in midtransition (the correlation coefficient being as high as 0.78). This means that the presented theory (having no adjustable parameters at all) is consistent with the experimental observations.

Kinetics↗

PubMed2001

Folding nuclei in proteins.

When a protein folds or unfolds, it passes through many half-folded microstates. Only a few of them can accumulate and be seen experimentally, and this happens only when the folding (or unfolding) occurs far from the point of thermodynamic equilibrium between the native and denatured states. The universal features of folding, though, are observed just close to the equilibrium point. Here the 'two-state' transition proceeds without any accumulation of metastable intermediates, and only the transition state ('folding nucleus') is outlined by its key influence on the folding-unfolding kinetics. Our aim is to review recent experimental and theoretical studies of the folding nuclei.

Kinetics↗

PubMed2000

Folding nuclei in 3D protein structures.

This paper presents and analyzes the results of several new approaches to the problem of finding the folding nucleus in a given 3D protein structure. Firstly, we show that the participation of residues in the hydrophobic core and the secondary structure of native protein has a rather modest correlation with the experimentally found phi values characterizing the participation of residues in the folding nuclei. Then we tried to find the nuclei as the free energy saddle points on the network of the folding/unfolding pathways using the branch-and-bound technique and dynamic programming. We also attempted to estimate the phi values from solving of kinetic equations for the network of protein folding/unfolding pathways. These approaches give a better correlation with experiment, and the estimated folding time is consistent with the experimentally observed rapid folding of small proteins.

Computer Simulation↗

PubMedDate not supplied

[Kinetics of folding nuclei formation in proteins].

When a protein folds or unfolds, it passes through many half-folded microstates. Only a few of them can accumulate and be seen experimentally, and this happens only when the folding (or unfolding) occurs far from the point of thermodynamic equilibrium between the native and denatured states. The universal features of folding, though, are observed in the vicinity of the equilibrium point. Here the "two-state" transition proceeds without any accumulation of metastable intermediates, and only the transition state ("folding nucleus") is outlined by its key influence on the folding/unfolding kinetics. This review covers recent experimental and theoretical studies of folding nuclei.

Animals↗