protein foldingLevinthal paradoxloop fold structureclosed loopsevolutionary conservationfolding nucleusWe show that loops of close contacts involving hydrophobic residues are important in protein folding. Contrary to Berezovsky and Trifonov (J. Biomol. Struct. Dyn. 20, 56, 2002) the loops important in ...
Protein folds and domains, structural motifs and connectivity between secondary structure elements, helices and sheets
We are now entering a new era in protein sequence and structure annotation, with hundreds of millions of predicted protein structures made available through the AlphaFold database1. These models cover nearly all proteins that are known, including those challenging to annotate for function or putative...
A fundamental question in protein evolution is whether nature has exhaustively sampled nearly all possible protein folds throughout evolution, or whether a large fraction of the possible folds remains unexplored. To address this question, we defined a se
Additionally what is important are not single loop contacts, but a highly interconnected network of such loop contacts, which provides extra stability to a protein fold and which leads to their conservation in evolution. 展开 关键词: protein folding Levinthal paradox loop fold structure closed ...
But before significant progress can be made, we have to make sense of the apparently chaotic sea of known protein structures. In the last few years, thanks to the newly developed techniques of structure analysis, a dramatic increase in the number of known protein structures has been achieved. ...
The function of proteins is a direct consequence of their three-dimensional structure. The structural classification of proteins describes the ways of folding patterns all proteins could adopt. Although, the protein folds were described in many ways the functional properties of individual folds were not...
The extension of the PEVK segment of the giant elastic protein titin is a key event in the elastic response of striated muscle to passive stretch. PEVK behaves mechanically as an entropic spring and is thought to be a random coil. cDNA sequencing of human fetal skeletal PEVK reveals a ...
The successful discrimination of protein folds would help to improve the accuracy of protein 3D structure prediction. Results: In this work, we propose a method based on linear discriminant analysis (LDA) for recognizing proteins belonging to 30 different folds using the occurrence of amino acid ...
Each protein domain has a fold, which refers to the arrangement of secondary structure elements in that domain. Relatively few distinct folds exist with respect to the number of protein sequences; accordingly, one fold may be utilized by many different proteins to perform a range of functions. ...