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Lin and her lab use computational chemistry to provide information on the solution structures of cyclic peptides. [2] They recently successfully used molecular dynamics simulation with enhanced sampling methods to design well-structured cyclic peptides. [12] [13]
Pentapeptide repeats were initially predicted from sequence to possess a right handed beta helix with three sides. [3] The first crystal structure of a pentapeptide repeat protein was the MfpA protein solved by Hegde and colleagues.
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A number of natural antimicrobial peptides are cyclic, and the products of SICLOPPS are "increasingly viewed as ideal backbones for modulation of protein-protein interactions." [ 3 ] Circular peptides tend to be resistant to protease activity, and may be suitable for use as orally administered drugs.
Each nonribosomal peptide synthetase can synthesize only one type of peptide. Nonribosomal peptides often have cyclic and/or branched structures, can contain non-proteinogenic amino acids including D-amino acids, carry modifications like N-methyl and N-formyl groups, or are glycosylated, acylated, halogenated, or hydroxylated.
The longest published result of a simulation performed using Anton as of 2011 was a 2.936 millisecond simulation of NTL9 at 355 K. [89] Such simulations are currently able to unfold and refold small proteins (<150 amino acids residues) in equilibrium and predict how mutations affect folding kinetics and stability.
The CyBase database collects proteins that are cyclic, some of which are permuted variants of cyclic wild-type proteins. [10] SISYPHUS is a database that contains a collection of hand-curated manual alignments of proteins with non-trivial relationships, several of which have circular permutations. [11]
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