Literature DB >> 28297652

Moving in the Right Direction: Protein Vibrations Steering Function.

Katherine A Niessen1, Mengyang Xu2, Alessandro Paciaroni3, Andrea Orecchini4, Edward H Snell5, Andrea G Markelz6.   

Abstract

Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.
Copyright © 2017. Published by Elsevier Inc.

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Year:  2017        PMID: 28297652      PMCID: PMC5355481          DOI: 10.1016/j.bpj.2016.12.049

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  51 in total

1.  Vibrational dynamics of myoglobin determined by the phonon-assisted Mössbauer effect.

Authors:  K Achterhold; C Keppler; A Ostermann; U van Bürck; W Sturhahn; E E Alp; F G Parak
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-05-17

Review 2.  Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

Authors:  Florence Tama; Charles L Brooks
Journal:  Annu Rev Biophys Biomol Struct       Date:  2006

3.  Intrinsic motions along an enzymatic reaction trajectory.

Authors:  Katherine A Henzler-Wildman; Vu Thai; Ming Lei; Maria Ott; Magnus Wolf-Watz; Tim Fenn; Ed Pozharski; Mark A Wilson; Gregory A Petsko; Martin Karplus; Christian G Hübner; Dorothee Kern
Journal:  Nature       Date:  2007-11-18       Impact factor: 49.962

4.  CHARMM-GUI: a web-based graphical user interface for CHARMM.

Authors:  Sunhwan Jo; Taehoon Kim; Vidyashankara G Iyer; Wonpil Im
Journal:  J Comput Chem       Date:  2008-08       Impact factor: 3.376

5.  Studies of phononlike low-energy excitations of protein molecules by inelastic x-ray scattering.

Authors:  Dazhi Liu; Xiang-qiang Chu; Marco Lagi; Yang Zhang; Emiliano Fratini; Piero Baglioni; Ahmet Alatas; Ayman Said; Ercan Alp; Sow-Hsin Chen
Journal:  Phys Rev Lett       Date:  2008-09-24       Impact factor: 9.161

Review 6.  Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.

Authors:  Lidio Meireles; Mert Gur; Ahmet Bakan; Ivet Bahar
Journal:  Protein Sci       Date:  2011-09-09       Impact factor: 6.725

7.  The hinge-bending mode of a lysozyme-inhibitor complex.

Authors:  R E Bruccoleri; M Karplus; J A McCammon
Journal:  Biopolymers       Date:  1986-09       Impact factor: 2.505

8.  Protein dynamics and enzymatic chemical barrier passage.

Authors:  Dimitri Antoniou; Steven D Schwartz
Journal:  J Phys Chem B       Date:  2011-11-15       Impact factor: 2.991

9.  Intermolecular vibrations in hydrophobic amino acid crystals: experiments and calculations.

Authors:  Michael R C Williams; Daniel J Aschaffenburg; Benjamin K Ofori-Okai; Charles A Schmuttenmaer
Journal:  J Phys Chem B       Date:  2013-08-28       Impact factor: 2.991

10.  Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.

Authors:  Matteo Levantino; Giorgio Schirò; Henrik Till Lemke; Grazia Cottone; James Michael Glownia; Diling Zhu; Mathieu Chollet; Hyotcherl Ihee; Antonio Cupane; Marco Cammarata
Journal:  Nat Commun       Date:  2015-04-02       Impact factor: 14.919

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  15 in total

1.  Tunable compact narrow band THz sources for frequency domain THz anisotropic spectroscopy.

Authors:  D K George; T J LaFAve; A G Markelz; Ian McNee; Peter Schunemann
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2019-05-13

2.  THz Anisotropy Identification using Tunable Compact Narrow Band THz Sources.

Authors:  D K George; A G Markelz; Ian Mcnee; Patrick Tekavec; Vladimir Kozlov; Peter Schunemann
Journal:  Int Conf Infrared Millim Terahertz Waves       Date:  2018-10-29

3.  Pickin' Up Good Vibrations.

Authors:  Jeremy C Smith
Journal:  Biophys J       Date:  2017-03-14       Impact factor: 4.033

4.  Near-field THz micropolarimetry.

Authors:  Katherine Niessen; Yanting Deng; A G Markelz
Journal:  Opt Express       Date:  2019-09-30       Impact factor: 3.894

5.  Stationary Sample Anisotropic THz Spectroscopy using Discretely Tunable THz Sources.

Authors:  T LaFave; D K George; A G Markelz; Ian McNee; Vladimir Kozlov; Peter Schunemann
Journal:  Int Conf Infrared Millim Terahertz Waves       Date:  2019-10-21

6.  Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.

Authors:  Daniel W Kneller; Oksana Gerlits; Luke L Daemen; Anna Pavlova; James C Gumbart; Yongqiang Cheng; Andrey Kovalevsky
Journal:  Phys Chem Chem Phys       Date:  2022-02-09       Impact factor: 3.676

7.  Molecular Dynamics Simulations of Macromolecular Crystals.

Authors:  David S Cerutti; David A Case
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2018-11-16

8.  Terahertz Spectroscopy Tracks Proteolysis by a Joint Analysis of Absorptance and Debye Model.

Authors:  Can Cao; Kazunori Serita; Keiko Kitagishi; Hironaru Murakami; Zhao-Hui Zhang; Masayoshi Tonouchi
Journal:  Biophys J       Date:  2020-11-13       Impact factor: 4.033

9.  Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids.

Authors:  Mario González-Jiménez; Gopakumar Ramakrishnan; Nikita V Tukachev; Hans M Senn; Klaas Wynne
Journal:  Phys Chem Chem Phys       Date:  2021-06-04       Impact factor: 3.676

10.  Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains.

Authors:  Valeria Conti Nibali; Giulia Morra; Martina Havenith; Giorgio Colombo
Journal:  J Phys Chem B       Date:  2017-10-31       Impact factor: 2.991

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