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Conformational isomerism

About: Conformational isomerism is a research topic. Over the lifetime, 11563 publications have been published within this topic receiving 199312 citations.


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Journal ArticleDOI
01 Jun 2001-Proteins
TL;DR: The major conclusion from this study is that salt bridges observed in crystal structure may break, and new salt bridges may be formed.
Abstract: This report investigates the effect of systemic protein conformational flexibility on the contribution of ion pairs to protein stability. Toward this goal, we use all NMR conformer ensembles in the Protein Data Bank (1) that contain at least 40 conformers, (2) whose functional form is monomeric, (3) that are nonredundant, and (4) that are large enough. We find 11 proteins adhering to these criteria. Within these proteins, we identify 22 ion pairs that are close enough to be classified as salt bridges. These are identified in the high-resolution crystal structures of the respective proteins or in the minimized average structures (if the crystal structures are unavailable) or, if both are unavailable, in the “most representative” conformer of each of the ensembles. We next calculate the electrostatic contribution of each such ion pair in each of the conformers in the ensembles. This results in a comprehensive study of 1,201 ion pairs, which allows us to look for consistent trends in their electrostatic contributions to protein stability in large sets of conformers. We find that the contributions of ion pairs vary considerably among the conformers of each protein. The vast majority of the ion pairs interconvert between being stabilizing and destabilizing to the structure at least once in the ensembles. These fluctuations reflect the variabilities in the location of the ion pairing residues and in the geometric orientation of these residues, both with respect to each other, and with respect to other charged groups in the remainder of the protein. The higher crystallographic B-factors for the respective side-chains are consistent with these fluctuations. The major conclusion from this study is that salt bridges observed in crystal structure may break, and new salt bridges may be formed. Hence, the overall stabilizing (or, destabilizing) contribution of an ion pair is conformer population dependent. Proteins 2001;43:433–454. © 2001 Wiley-Liss, Inc.

48 citations

Journal ArticleDOI
TL;DR: In this article, the four stable conformers of N-methylacetamide that result from conformational isomerism of the CH, groups were obtained, at the 4-31G* level.

48 citations

Journal ArticleDOI
TL;DR: In this paper, the force-extension measurements on simple poly(ethylene glycol) molecules in different solvents can be quantitatively explained based on ab initio quantum mechanical calculations of the potential energy surfaces of the polymer segments in vacuum and in the solvated form.
Abstract: The force-extension measurements on simple poly(ethylene glycol) molecules by Oesterfelt et al in different solvents can be quantitatively explained based on ab initio quantum mechanical calculations of the potential energy surfaces of the polymer segments in vacuum and in the solvated form. The proper statistical mechanical calculations of the force-extension relation, both for isothermal-isochoric and isothermal-isobaric conditions (the latter appropriate to the experimental set-up), demonstrate, that in the low-force regime transitions from the amorphous to the helical conformers, and in the high-force regime stretching of the helical to the planar `all-trans' conformer occur. The presence of water affects all but the `all-trans' conformer by shortening and stiffening.

48 citations

Journal ArticleDOI
TL;DR: The vicinal31P-O-C-1H couplings of a series of acyclic phosphate esters have been measured and rationalized in terms of varying populations of individual rotamers as mentioned in this paper.
Abstract: The vicinal31P—O—C—1H couplings of a series of acyclic phosphate esters have been measured and rationalized in terms of varying populations of individual rotamers. Variable temperature measurements have been interpreted in terms of the enthalpy and entropy differences between gauche and trans rotational isomers.

48 citations

Journal ArticleDOI
TL;DR: It is shown that there are no conformational obstacles for incorporation of d4U and d4C into the double helical A and B forms of DNA.
Abstract: A comprehensive quantum-chemical conformational analysis of two nucleoside analogues, 2′,3′-didehydro-2′,3′-dideoxyuridine (d4U) and 2′,3′-didehydro-2′,3′-dideoxycytidine (d4C), is reported. The electronic structure calculations were performed at the MP2/6-311++G(d,p)//B3LYP/6-31++G(d,p) level of theory. It was found that d4U and d4C adopt 20 conformers and 19 conformers, respectively, which correspond to local minima on the respective potential energy landscapes. QTAIM and NBO analyses show that the d4U and d4C conformers are stabilised by a complicated network of specific intramolecular interactions, which includes conventional (OH⋯O) and non-conventional (CH⋯O, CH⋯HC) H-bonds as well as closed-shell van der Waals (C⋯O) contacts. A satisfactory linear correlation was found between Grunenberg's compliance constants for closed-shell intramolecular interactions and their energy. It is shown that there are no conformational obstacles for incorporation of d4U and d4C into the double helical A and B forms of DNA. The less pronounced biological activity of d4U as compared to 2′,3′-didehydro-2′,3′-dideoxythymidine (d4T) is most likely due to the presence of the bulky methyl group at the 5-position of d4T, which can be recognised by target enzymes.

48 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023303
2022618
2021217
2020219
2019228
2018268