Protein energy landscape

The protein energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. Reconstructing a protein’s energy landscape holds the key to characterizing a protein’s equilibrium conformational dynamics and its relationship to function. Many pathogenic mutations in protein sequences alter the equilibrium dynamics that regulates molecular interactions and thus protein function.

13p vitzuyu2711 29-09-2021 15 1   Download

Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and non-native decoys) in a decoy set makes the problem even more complicated.

21p viwyoming2711 16-12-2020 9 1   Download

Understanding protein structure and dynamics is essential for understanding their function. This is a challenging task due to the high complexity of the conformational landscapes of proteins and their rugged energy levels. In particular, it is important to detect highly populated regions which could correspond to intermediate structures or local minima.

9p viconnecticut2711 29-10-2020 13 1   Download

Computational approaches for the determination of biologically-active/native three-dimensional structures of proteins with novel sequences have to handle several challenges. The (conformation) space of possible three-dimensional spatial arrangements of the chain of amino acids that constitute a protein molecule is vast and highdimensional.

17p vijisoo2711 27-10-2020 12 0   Download

A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones.

13p vicolorado2711 23-10-2020 11 3   Download

The transition state region on the free energy surface then was sampled by using umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

11p viaphrodite2711 14-10-2019 14 1   Download

In this study, we investigate the role of amino a id sequen es in the folding of proteins. We onsider two models that are diered by sequen espe iity: the tube HP model with hydrophobi (H) and polar (P) sequen es, and the tube Go model with native- entri onta t potentials

7p thuyliebe 12-10-2018 19 0   Download