2012
DOI: 10.1021/jp207807a
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Comprehensive Conformational Studies of Five Tripeptides and a Deduced Method for Efficient Determinations of Peptide Structures

Abstract: Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semi-empirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for fi… Show more

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Cited by 17 publications
(33 citation statements)
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“…The majority of the configurations are curly, so our transferability tests are severe. Finally we note that, although not directly investigated here, it is well known that the number of local energy minima present in oligopeptide conformational space is vast [56]. Based on the data presented here, we cannot be sure that the fixed configurations studied are representative for configurations found in the Protein Data Bank, for example.…”
Section: Resultsmentioning
confidence: 76%
“…The majority of the configurations are curly, so our transferability tests are severe. Finally we note that, although not directly investigated here, it is well known that the number of local energy minima present in oligopeptide conformational space is vast [56]. Based on the data presented here, we cannot be sure that the fixed configurations studied are representative for configurations found in the Protein Data Bank, for example.…”
Section: Resultsmentioning
confidence: 76%
“…Polyglycine peptides are model systems which were extensively studied experimentally (Wu & Fenselau, ; Cheng, Wu, & Fenselau, ; Zhang et al, ; Wu & Lebrilla (, ); Hudgins et al, ; Wu & McMahon, ) and theoretically (Zhang et al, ; Zhang, Cassady, & Chung‐Philips, ; Cassady et al, ; Strittmatter & Williams, ; Rodriquez et al, ; Chung‐Philips, ; Wu & McMahon, , ; Wang et al, ; Ye & Armentrout, ; Toroz & van Mourik, ; Yu et al, ). Table summarizes the corresponding gas‐phase basicity results.…”
Section: Acids and Derivativesmentioning
confidence: 99%
“…We choose to present here computational results on the triglycine system as a typical example. Extensive computational search for neutral GGG conformers has been performed during the last years (Strittmatter & Williams, ; Rodriquez et al, ; Chung‐Philips, ; Wang et al, ; Wu & McMahon, 2007, ; Ye & Armentrout, ; Toroz & van Mourik, ; Yu et al, ). As expected, results are depending upon the strategy and the level of theory used to explore the potential energy surface.…”
Section: Acids and Derivativesmentioning
confidence: 99%
“…The systematic structural search method is quite reliable as it considers combinations of all bond rotational degrees of freedom of biomolecule 1 . However, the computational cost of the systematic approach increases exponentially with the size of the molecule and it is applicable to very small peptides 2 , 3 . The stochastic approach searches the bimolecular structure by sampling its potential energy surface (PES) in some designated way, such as simulated annealing 4 6 , Monte-Carlo 7 9 , genetic algorithm 10 12 , and basin-hopping 13 , 14 .…”
Section: Introductionmentioning
confidence: 99%
“…The “divide and conquer” search method first divides a peptide into smaller peptide fragments whose conformations may be reliably determined by, say, a systematic structural search method. The conformations of the constituting peptide fragments are then properly combined to yield the low energy conformations of the target peptide 2 , 15 , 16 . The “divide and conquer” method possess a highly desirable feature that the required computational cost increases moderately with the number of amino acid (AA) residues in a peptide 2 , 17 .…”
Section: Introductionmentioning
confidence: 99%