Literature DB >> 28060489

Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.

Ayanjeet Ghosh1, Joshua S Ostrander1, Martin T Zanni1.   

Abstract

Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.

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Year:  2017        PMID: 28060489      PMCID: PMC5500453          DOI: 10.1021/acs.chemrev.6b00582

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  243 in total

Review 1.  Fast kinetics and mechanisms in protein folding.

Authors:  W A Eaton; V Muñoz; S J Hagen; G S Jas; L J Lapidus; E R Henry; J Hofrichter
Journal:  Annu Rev Biophys Biomol Struct       Date:  2000

2.  Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.

Authors:  Kusai A Merchant; W G Noid; Ryo Akiyama; Ilya J Finkelstein; Alexei Goun; Brian L McClain; Roger F Loring; M D Fayer
Journal:  J Am Chem Soc       Date:  2003-11-12       Impact factor: 15.419

3.  Deamidation accelerates amyloid formation and alters amylin fiber structure.

Authors:  Emily B Dunkelberger; Lauren E Buchanan; Peter Marek; Ping Cao; Daniel P Raleigh; Martin T Zanni
Journal:  J Am Chem Soc       Date:  2012-07-17       Impact factor: 15.419

4.  Chemical exchange 2D IR of hydrogen-bond making and breaking.

Authors:  Yung Sam Kim; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2005-07-22       Impact factor: 11.205

5.  Characterization of spectral diffusion from two-dimensional line shapes.

Authors:  Sean T Roberts; Joseph J Loparo; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2006-08-28       Impact factor: 3.488

6.  A unified model of protein dynamics.

Authors:  Hans Frauenfelder; Guo Chen; Joel Berendzen; Paul W Fenimore; Helén Jansson; Benjamin H McMahon; Izabela R Stroe; Jan Swenson; Robert D Young
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-27       Impact factor: 11.205

7.  Exposing the Moving Parts of Proteins with NMR Spectroscopy.

Authors:  J W Peng
Journal:  J Phys Chem Lett       Date:  2012-04-02       Impact factor: 6.475

8.  Structural dynamics inside a functionalized metal-organic framework probed by ultrafast 2D IR spectroscopy.

Authors:  Jun Nishida; Amr Tamimi; Honghan Fei; Sonja Pullen; Sascha Ott; Seth M Cohen; Michael D Fayer
Journal:  Proc Natl Acad Sci U S A       Date:  2014-12-15       Impact factor: 11.205

9.  Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor.

Authors:  Chris T Middleton; Peter Marek; Ping Cao; Chi-cheng Chiu; Sadanand Singh; Ann Marie Woys; Juan J de Pablo; Daniel P Raleigh; Martin T Zanni
Journal:  Nat Chem       Date:  2012-03-11       Impact factor: 24.427

10.  Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

Authors:  Biswajit Guchhait; Yingliang Liu; Torsten Siebert; Thomas Elsaesser
Journal:  Struct Dyn       Date:  2015-12-08       Impact factor: 2.920

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  37 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

2.  Single-molecule FRET methods to study the dynamics of proteins at work.

Authors:  Hisham Mazal; Gilad Haran
Journal:  Curr Opin Biomed Eng       Date:  2019-08-23

3.  Physiological Calcium Concentrations Slow Dynamics at the Lipid-Water Interface.

Authors:  Mason L Valentine; Alfredo E Cardenas; Ron Elber; Carlos R Baiz
Journal:  Biophys J       Date:  2018-09-06       Impact factor: 4.033

4.  Transparent window 2D IR spectroscopy of proteins.

Authors:  Megan C Thielges
Journal:  J Chem Phys       Date:  2021-07-28       Impact factor: 3.488

5.  Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.

Authors:  Sashary Ramos; Megan C Thielges
Journal:  J Phys Chem B       Date:  2019-03-21       Impact factor: 2.991

6.  A Proposed Method to Obtain Surface Specificity with Pump-Probe and 2D Spectroscopies.

Authors:  Megan K Petti; Joshua S Ostrander; Erin R Birdsall; Miriam Bohlmann Kunz; Zachary T Armstrong; Ariel M Alperstein; Martin T Zanni
Journal:  J Phys Chem A       Date:  2020-04-16       Impact factor: 2.781

7.  Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity.

Authors:  Matthew G Roberson; Devin K Smith; Simon M White; Ian S Wallace; Matthew J Tucker
Journal:  Biophys J       Date:  2019-02-15       Impact factor: 4.033

8.  Deuterium-Enhanced Raman Spectroscopy for Histidine pKa Determination in a pH-Responsive Hydrogel.

Authors:  Gabriel A Braun; Brett H Pogostin; Milda Pucetaite; Casey H Londergan; Karin S Åkerfeldt
Journal:  Biophys J       Date:  2020-09-23       Impact factor: 4.033

9.  Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy.

Authors:  Justin P Lomont; Joshua S Ostrander; Jia-Jung Ho; Megan K Petti; Martin T Zanni
Journal:  J Phys Chem B       Date:  2017-09-19       Impact factor: 2.991

10.  Cavity hydration dynamics in cytochrome c oxidase and functional implications.

Authors:  Chang Yun Son; Arun Yethiraj; Qiang Cui
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-02       Impact factor: 11.205

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