2001
DOI: 10.1002/jcc.1062
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Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force field

Abstract: When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp 2 sulfur are required. In this article, parameters for the thioamide grou… Show more

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Cited by 9 publications
(5 citation statements)
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“…The X‐ray diffraction structures of both Ac‐Alat‐NHMe and Act‐Ala‐NHMe adopt β‐sheet conformation and exhibit similar hydrogen bonding patterns in which one molecular face is involved in two oxo hydrogen bonds and the molecular face is involved in two thio hydrogen bonds. The validity of our newly derived thioamide parameters (26) for the CFF91 force field was confirmed by three distinct assessments, all of which showed low deviation between the conformations obtained from X‐ray diffraction and the conformations obtained from theoretical calculations using the thioamide parameters.…”
Section: Resultsmentioning
confidence: 62%
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“…The X‐ray diffraction structures of both Ac‐Alat‐NHMe and Act‐Ala‐NHMe adopt β‐sheet conformation and exhibit similar hydrogen bonding patterns in which one molecular face is involved in two oxo hydrogen bonds and the molecular face is involved in two thio hydrogen bonds. The validity of our newly derived thioamide parameters (26) for the CFF91 force field was confirmed by three distinct assessments, all of which showed low deviation between the conformations obtained from X‐ray diffraction and the conformations obtained from theoretical calculations using the thioamide parameters.…”
Section: Resultsmentioning
confidence: 62%
“…The crystal structures for both Ac‐Alat‐NHMe and Act‐Ala‐NHMe provided an excellent opportunity for validating our recently derived CFF91 force field thioamide parameters (26,27) by comparing the calculated and the observed (φ, ψ) dihedral angles.…”
Section: Resultsmentioning
confidence: 97%
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“…Noncoding amino acids have also been used to restrict the conformational space of peptides, allowing more predictable peptide conformers to be constructed with potential increase in binding affinity. , Furthermore, noncoding amino acids have been used to confer resistance to enzymatic degradation within the body, to probe protein structures, in de novo design of protein, , to design structures with novel fold or secondary structure, , and to create new combinatorial chemistry libraries. When the oxygen of the peptide unit is replaced by a sp 2 sulfur atom, the thiopeptide formed becomes resistant to enzymatic degradation. , Thiopeptides have been used in structure activity relationship studies to alter biological activities, , and, in particular, a thio-enkephalin has been shown to have enhanced potency and a change in selectivity in both biological and binding assays . Our previous X-ray studies and conformational energy and free energy calculations of thio substituted dipeptides suggest they are more conformationally restricted than peptides and have distinctly different hydrogen bonding properties.…”
Section: Introductionmentioning
confidence: 99%