PMID: 8589611Sep 1, 1995Paper

Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor

Journal of Biomolecular NMR
A R FadelR M Levy

Abstract

Order parameters for the backbone N-H and C alpha-H bond vectors have been calculated from a 150 ps molecular dynamics (MD) simulation of human type-alpha transforming growth factor in H2O solvent. Two kinds of 'crankshaft motions' of the polypeptide backbone are observed in this MD trajectory. The first involves small-amplitude rocking of the rigid peptide bond due to correlated changes in the backbone dihedral angles psi i-1 and phi i. These high-frequency 'librational crankshaft' motions are correlated with systematically smaller values of motional order parameters for backbone N-H bond vectors compared to C alpha-H bond vectors. In addition, infrequent 'crankshaft flips' of the peptide bond from one local minimum to another are observed for several amino acid residues. These MD simulations demonstrate that comparisons of N-H and C alpha-H order parameters provide a useful approach for identifying crankshaft librational motions in proteins.

References

Jul 22, 1976·Nature·J A McCammonP G Wolynes
Jun 1, 1976·Biopolymers·M Go, N Go
Aug 15, 1983·Journal of Molecular Biology·M Levitt
Jul 1, 1994·Journal of Magnetic Resonance. Series B·S BalasubramanianP H Bolton

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Citations

Aug 7, 2002·Journal of Molecular Biology·Mark BerjanskiiSteven R Van Doren
Oct 14, 2009·Journal of the American Chemical Society·Devon SheppardVitali Tugarinov
Dec 18, 2010·The Journal of Physical Chemistry. B·Eva MeirovitchJack H Freed
Dec 6, 2001·European Journal of Biochemistry·S G ChamberlinD L Turner
Aug 10, 2012·PLoS Computational Biology·Daniel A KeedyJane S Richardson
Mar 25, 2010·The Journal of Chemical Physics·Satoshi OmoriAkinori Kidera
Oct 28, 2015·PLoS Computational Biology·Daniel A KeedyHenry van den Bedem
Jun 23, 2016·Journal of the American Chemical Society·R Bryn FenwickBeat Vögeli
Jan 1, 1996·Annual Review of Physical Chemistry·K T DayieJ F Lefèvre
Jan 18, 2008·Biophysical Journal·Ibon IloroBelinda Pastrana-Ríos
Feb 14, 2006·Structure·Ian W DavisJane S Richardson
Jun 12, 2014·Nature Communications·R Bryn FenwickXavier Salvatella
Jan 23, 2003·Protein Science : a Publication of the Protein Society·Bernard GilquinAndré Ménez
Oct 3, 2006·Journal of Biomolecular NMR·Tianzhi WangErik R P Zuiderweg
Apr 22, 2005·Angewandte Chemie·Phineus R L MarkwickMichael Sattler
Apr 18, 2009·Journal of Computational Chemistry·Satoshi OmoriAkinori Kidera
Jan 30, 2014·Proceedings of the National Academy of Sciences of the United States of America·R Bryn FenwickPeter E Wright
Jul 16, 2013·Chemistry : a European Journal·Carsten BaldaufMatthias Scheffler
Jan 12, 2021·Chemical Reviews·Jovan DamjanovicYu-Shan Lin
Sep 17, 2004·Journal of the American Chemical Society·Tobias S UlmerAd Bax
Jun 9, 2021·The Journal of Physical Chemistry. B·Netanel Mendelman, Eva Meirovitch
Apr 20, 2012·The Journal of Physical Chemistry. B·Eva MeirovitchChristian Griesinger
Dec 1, 2011·The Journal of Physical Chemistry. B·Eva MeirovitchAntonino Polimeno
Mar 7, 2019·The Journal of Physical Chemistry. B·Oren TchaicheeyanEva Meirovitch
Apr 2, 2008·The Journal of Physical Chemistry. B·Eric JohnsonRafael Brüschweiler
Feb 13, 2003·Journal of the American Chemical Society·Wing-Yiu ChoyLewis E Kay
Jul 20, 2007·Journal of the American Chemical Society·Sebastian MeierMartin Blackledge
Oct 8, 2021·Proceedings of the National Academy of Sciences of the United States of America·Dhiman RayIoan Andricioaei

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