Topic
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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TL;DR: The present results show that the magnitude of epsilon(t) in right-handed ribo helices is confined to the range 214 degrees-226 degrees, which is in much better agreement with single crystal X-ray studies than were previous deductions from NMR spectroscopic results.
Abstract: 13C-31P coupling constants of 10 oligoribonucleoside phosphates, measured at a number of temperatures, are presented. The combination of these data with 1H-31P couplings of the same compounds leads to the derivation of two new and mutually consistent sets of Karplus parameters: J(CCOP) = 6.9cos2 phi--3.4cos phi + 0.7 J(HCOP) = 15.3cos2 phi--6.1cos phi + 1.6 At the same time new values for the base sequence dependent magnitude of the trans conformer of the backbone angle epsilon (C4'-C3'-O3'-P) are calculated. The present results show that the magnitude of epsilon(t) in right-handed ribo helices is confined to the range 214 degrees-226 degrees (average 219 degrees), which is in much better agreement with single crystal X-ray studies (average 218 degrees) than were previous deductions from NMR spectroscopic results (average 208 degrees).
194 citations
TL;DR: A new method for including local conformational flexibility in calculations of the hydrogen ion titration of proteins using macroscopic electrostatic models is presented, with significantly improved agreement with experiment and reduced sensitivity of the intrinsic pKa calculations to the initial details of the structure compared to single-conformer calculations.
193 citations
TL;DR: The conformational structures of tryptophan, isolated in the gas phase, have been assigned by combining the results of ultraviolet hole-burning and infrared ion dip spectroscopy with the predictions of ab initio calculations conducted at the MP2/6-311 + G(d,p)//B3LYP/6 −31 + G (d) levels of theory as discussed by the authors.
Abstract: The conformational structures of tryptophan, isolated in the gas phase, have been assigned by combining
the results of ultraviolet hole-burning and infrared ion dip spectroscopy with the predictions of ab initio
calculations conducted at the MP2/6-311 + G(d,p)//B3LYP/6-31 + G(d) levels of theory. As in phenylalanine, the
most strongly populated, and lowest energy conformer presents a folded alanyl side chain that is stabilised by a ‘daisy chain’ of hydrogen-bonded interactions. These link the acidic proton, the amino group and the indole ring. There is a further interaction between the carbonyl oxygen and the neighbouring CH group on the pyrrole ring. A quantitative evaluation of the dipole–dipole interactions between the alanyl side chain and the indole ring in the 1La and 1Lb electronic states does not support the suggestion of electronic state mixing. In
particular it casts doubt on the assignment of the fluorescence of the most
stable, ‘special’ conformer to emission from the 1La state.
192 citations
TL;DR: The region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average, and it is demonstrated that these induced-fit structural adjustments are comparable in magnitude to conformational selection.
Abstract: Noncovalent binding interactions between proteins are the central physicochemical phenomenon underlying biological signaling and functional control on the molecular level. Here, we perform an extensive structural analysis of a large set of bound and unbound ubiquitin conformers and study the level of residual induced fit after conformational selection in the binding process. We show that the region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average. We demonstrate that these induced-fit structural adjustments are comparable in magnitude to conformational selection. Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions.
191 citations
TL;DR: The enthalpy for conformational change from nonplanar to planar EMI+ experimentally obtained by analyzing band intensities of the conformers at varying temperatures is practically the same as that evaluated by theoretical calculations.
Abstract: Raman spectra of liquid 1-ethyl-3-methylimidazolium (EMI+) salts, EMI+BF4-, EMI+PF6-, EMI+CF3SO3-, and EMI+N(CF3SO2)2-, were measured over the frequency range 200−1600 cm-1. In the range 200−500 cm-1, we found five bands originating from the EMI+ ion at 241, 297, 387, 430, and 448 cm-1. However, the 448 cm-1 band could hardly be reproduced by theoretical calculations in terms of a given EMI+ conformer, implying that the band originates from another conformer. This is expected because the EMI+ involves an ethyl group bound to the N atom of the imidazolium ring, and the ethyl group can rotate along the C−N bond to yield conformers. The torsion energy for the rotation was then theoretically calculated. Two local minima with an energy difference of ca. 2 kJ mol-1 were found, suggesting that two conformers are present in equilibrium. Full geometry optimizations followed by normal frequency analyses indicate that the two conformers are those with planar and nonplanar ethyl groups against the imidazolium ring pl...
191 citations