Literature DB >> 25580624

Site-specific infrared probes of proteins.

Jianqiang Ma1, Ileana M Pazos, Wenkai Zhang, Robert M Culik, Feng Gai.   

Abstract

Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.

Entities:  

Keywords:  infrared spectroscopy; isotope editing; site-specific probe; unnatural amino acid; vibrational Stark effect spectroscopy; vibrational coupling

Mesh:

Substances:

Year:  2015        PMID: 25580624      PMCID: PMC4382430          DOI: 10.1146/annurev-physchem-040214-121802

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  136 in total

1.  Energy transport in peptide helices: a comparison between high- and low-energy excitations.

Authors:  Ellen H G Backus; Phuong H Nguyen; Virgiliu Botan; Rolf Pfister; Alessandro Moretto; Marco Crisma; Claudio Toniolo; Gerhard Stock; Peter Hamm
Journal:  J Phys Chem B       Date:  2008-07-03       Impact factor: 2.991

2.  Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes.

Authors:  Stephen D Fried; Sayan Bagchi; Steven G Boxer
Journal:  J Am Chem Soc       Date:  2013-07-18       Impact factor: 15.419

3.  Tidal surge in the M2 proton channel, sensed by 2D IR spectroscopy.

Authors:  Ayanjeet Ghosh; Jade Qiu; William F DeGrado; Robin M Hochstrasser
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-28       Impact factor: 11.205

4.  3-picolyl azide adenine dinucleotide as a probe of femtosecond to picosecond enzyme dynamics.

Authors:  Samrat Dutta; Yun-Liang Li; William Rock; Jon C D Houtman; Amnon Kohen; Christopher M Cheatum
Journal:  J Phys Chem B       Date:  2011-12-15       Impact factor: 2.991

5.  Modulation of p-cyanophenylalanine fluorescence by amino acid side chains and rational design of fluorescence probes of alpha-helix formation.

Authors:  Humeyra Taskent-Sezgin; Peter Marek; Rosanne Thomas; Daniel Goldberg; Juah Chung; Isaac Carrico; Daniel P Raleigh
Journal:  Biochemistry       Date:  2010-07-27       Impact factor: 3.162

6.  Ribonuclease S dynamics measured using a nitrile label with 2D IR vibrational echo spectroscopy.

Authors:  Sayan Bagchi; Steven G Boxer; Michael D Fayer
Journal:  J Phys Chem B       Date:  2012-03-23       Impact factor: 2.991

7.  A direct comparison of azide and nitrile vibrational probes.

Authors:  Xin Sonia Gai; Basil A Coutifaris; Scott H Brewer; Edward E Fenlon
Journal:  Phys Chem Chem Phys       Date:  2011-02-18       Impact factor: 3.676

8.  Photophysics of a Fluorescent Non-natural Amino Acid: p-Cyanophenylalanine.

Authors:  Arnaldo L Serrano; Thomas Troxler; Matthew J Tucker; Feng Gai
Journal:  Chem Phys Lett       Date:  2010-03-05       Impact factor: 2.328

9.  Amide-I characteristics of helical β-peptides by linear infrared measurement and computations.

Authors:  Juan Zhao; Jipei Shi; Jianping Wang
Journal:  J Phys Chem B       Date:  2013-12-23       Impact factor: 2.991

10.  Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.

Authors:  C Tony Liu; Joshua P Layfield; Robert J Stewart; Jarrod B French; Philip Hanoian; John B Asbury; Sharon Hammes-Schiffer; Stephen J Benkovic
Journal:  J Am Chem Soc       Date:  2014-07-11       Impact factor: 15.419

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  38 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.  Sensing pH via p-cyanophenylalanine fluorescence: Application to determine peptide pKa and membrane penetration kinetics.

Authors:  Ileana M Pazos; Ismail A Ahmed; Mariana I León Berríos; Feng Gai
Journal:  Anal Biochem       Date:  2015-04-29       Impact factor: 3.365

3.  Mapping fast protein folding with multiple-site fluorescent probes.

Authors:  Maxim B Prigozhin; Shu-Han Chao; Shahar Sukenik; Taras V Pogorelov; Martin Gruebele
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-15       Impact factor: 11.205

Review 4.  Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.

Authors:  Ayanjeet Ghosh; Joshua S Ostrander; Martin T Zanni
Journal:  Chem Rev       Date:  2017-01-06       Impact factor: 60.622

Review 5.  Meandering Down the Energy Landscape of Protein Folding: Are We There Yet?

Authors:  Rachel M Abaskharon; Feng Gai
Journal:  Biophys J       Date:  2016-05-10       Impact factor: 4.033

Review 6.  Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes.

Authors:  Lu Wei; Fanghao Hu; Zhixing Chen; Yihui Shen; Luyuan Zhang; Wei Min
Journal:  Acc Chem Res       Date:  2016-08-03       Impact factor: 22.384

7.  Non-Additive Effects of Binding Site Mutations in Calmodulin.

Authors:  Sean C Edington; D Brent Halling; Suzanna M Bennett; Thomas R Middendorf; Richard W Aldrich; Carlos R Baiz
Journal:  Biochemistry       Date:  2019-06-04       Impact factor: 3.162

8.  Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine.

Authors:  Nicole Maurici; Nicole Savidge; Byung Uk Lee; Scott H Brewer; Christine M Phillips-Piro
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-09-19       Impact factor: 1.056

9.  Ultrafast Dynamics at Lipid-Water Interfaces.

Authors:  Jennifer C Flanagan; Mason L Valentine; Carlos R Baiz
Journal:  Acc Chem Res       Date:  2020-08-31       Impact factor: 22.384

10.  Extending the vibrational lifetime of azides with heavy atoms.

Authors:  Farzaneh Chalyavi; Andrew J Schmitz; Natalie R Fetto; Matthew J Tucker; Scott H Brewer; Edward E Fenlon
Journal:  Phys Chem Chem Phys       Date:  2020-08-24       Impact factor: 3.676

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