Literature DB >> 16147526

Quantum chemical studies of protein structure.

Eric Oldfield1.   

Abstract

Quantum chemical methods now permit the prediction of many spectroscopic observables in proteins and related model systems, in addition to electrostatic properties, which are found to be in excellent accord with those determined from experiment. I discuss the developments over the past decade in these areas, including predictions of nuclear magnetic resonance chemical shifts, chemical shielding tensors, scalar couplings and hyperfine (contact) shifts, the isomer shifts and quadrupole splittings in Mössbauer spectroscopy, molecular energies and conformations, as well as a range of electrostatic properties, such as charge densities, the curvatures, Laplacians and Hessians of the charge density, electrostatic potentials, electric field gradients and electrostatic field effects. The availability of structure/spectroscopic correlations from quantum chemistry provides a basis for using numerous spectroscopic observables in determining aspects of protein structure, in determining electrostatic properties which are not readily accessible from experiment, as well as giving additional confidence in the use of these techniques to investigate questions about chemical bonding and chemical reactions.

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Year:  2005        PMID: 16147526      PMCID: PMC1569496          DOI: 10.1098/rstb.2003.1421

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  34 in total

1.  A steric mechanism for inhibition of CO binding to heme proteins.

Authors:  G S Kachalova; A N Popov; H D Bartunik
Journal:  Science       Date:  1999-04-16       Impact factor: 47.728

2.  Topological properties of the peptide bond in glycyl-L-threonine dihydrate based on a fast synchrotron/CCD-diffraction experiment at 100 K.

Authors:  B Dittrich; R Flaig; T Koritsánszky; H G Krane; W Morgenroth; P Luger
Journal:  Chemistry       Date:  2000-07-14       Impact factor: 5.236

3.  (57)Fe Mössbauer isomer shifts of heme protein model systems: electronic structure calculations.

Authors:  Yong Zhang; Junhong Mao; Eric Oldfield
Journal:  J Am Chem Soc       Date:  2002-07-03       Impact factor: 15.419

4.  Unblocked statistical-coil tetrapeptides in aqueous solution: quantum-chemical computation of the carbon-13 NMR chemical shifts.

Authors:  Jorge A Vila; Héctor A Baldoni; Daniel R Ripoll; Harold A Scheraga
Journal:  J Biomol NMR       Date:  2003-06       Impact factor: 2.835

5.  The Shared-Electron Chemical Bond.

Authors:  L Pauling
Journal:  Proc Natl Acad Sci U S A       Date:  1928-04       Impact factor: 11.205

Review 6.  The use of chemical shifts and their anisotropies in biomolecular structure determination.

Authors:  D A Case
Journal:  Curr Opin Struct Biol       Date:  1998-10       Impact factor: 6.809

7.  Natrual-abundance carbon-13 nuclear magnetic resonance studies in 20-mm sample tubes. Observation of numerous single-carbon resonances of hen egg-white lysozyme.

Authors:  A Allerhand; R F Childers; E Oldfield
Journal:  Biochemistry       Date:  1973-03-27       Impact factor: 3.162

8.  Nuclear magnetic resonance shifts in paramagnetic metalloporphyrins and metalloproteins.

Authors:  Junhong Mao; Yong Zhang; Eric Oldfield
Journal:  J Am Chem Soc       Date:  2002-11-20       Impact factor: 15.419

9.  Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density.

Authors:  Xue Li; Guang Wu; Yuriy A Abramov; Anatoliy V Volkov; Philip Coppens
Journal:  Proc Natl Acad Sci U S A       Date:  2002-09-09       Impact factor: 11.205

10.  Determination of rotational mobilities of backbone and side-chain carbons of poly(gamma-benzyl L-glutamate) in the helical and random-coil states from measurements of carbon-13 relaxation times and nuclear Overhauser enhancements.

Authors:  A Allerhand; E Oldfield
Journal:  Biochemistry       Date:  1973-08-28       Impact factor: 3.162

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  13 in total

1.  Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties.

Authors:  Kevin E Riley; Bryan T Op't Holt; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2007       Impact factor: 6.006

2.  31P-dephased, 13C-detected REDOR for NMR crystallography at natural isotopic abundance.

Authors:  Alexander I Greenwood; Mary C Clay; Chad M Rienstra
Journal:  J Magn Reson       Date:  2017-02-28       Impact factor: 2.229

3.  Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics.

Authors:  Yu-ming M Huang; Myungshim Kang; Chia-en A Chang
Journal:  J Mol Recognit       Date:  2014-09       Impact factor: 2.137

4.  Evaluating electronic structure methods for accurate calculation of 19 F chemical shifts in fluorinated amino acids.

Authors:  Jayangika N Dahanayake; Chandana Kasireddy; Jonathan M Ellis; Derek Hildebrandt; Olivia A Hull; Joseph P Karnes; Dylan Morlan; Katie R Mitchell-Koch
Journal:  J Comput Chem       Date:  2017-08-21       Impact factor: 3.376

5.  77Se NMR Probes the Protein Environment of Selenomethionine.

Authors:  Qingqing Chen; Shiping Xu; Xingyu Lu; Michael V Boeri; Yuliya Pepelyayeva; Elizabeth L Diaz; Sunil-Datta Soni; Marc Allaire; Martin B Forstner; Brian J Bahnson; Sharon Rozovsky
Journal:  J Phys Chem B       Date:  2020-01-07       Impact factor: 2.991

6.  Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase.

Authors:  Yu-Ming M Huang; Wanli You; Bethany G Caulkins; Michael F Dunn; Leonard J Mueller; Chia-En A Chang
Journal:  Protein Sci       Date:  2015-09-22       Impact factor: 6.725

7.  Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF-3 rather than by phosphoranes.

Authors:  Nicola J Baxter; Matthew W Bowler; Tooba Alizadeh; Matthew J Cliff; Andrea M Hounslow; Bin Wu; David B Berkowitz; Nicholas H Williams; G Michael Blackburn; Jonathan P Waltho
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-17       Impact factor: 11.205

8.  Cytochrome-P450-cytochrome-b5 interaction in a membrane environment changes 15N chemical shift anisotropy tensors.

Authors:  Manoj Kumar Pandey; Subramanian Vivekanandan; Shivani Ahuja; Rui Huang; Sang-Choul Im; Lucy Waskell; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2013-10-28       Impact factor: 2.991

9.  Protein structure refinement using 13C alpha chemical shift tensors.

Authors:  Benjamin J Wylie; Charles D Schwieters; Eric Oldfield; Chad M Rienstra
Journal:  J Am Chem Soc       Date:  2009-01-28       Impact factor: 15.419

10.  Quantum chemical calculations of amide-15N chemical shift anisotropy tensors for a membrane-bound cytochrome-b5.

Authors:  Manoj Kumar Pandey; Ayyalusamy Ramamoorthy
Journal:  J Phys Chem B       Date:  2013-01-10       Impact factor: 2.991

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