Literature DB >> 22109973

Spectroscopic studies of protein folding: linear and nonlinear methods.

Arnaldo L Serrano1, Matthias M Waegele, Feng Gai.   

Abstract

Although protein folding is a simple outcome of the underlying thermodynamics, arriving at a quantitative and predictive understanding of how proteins fold nevertheless poses huge challenges. Therefore, both advanced experimental and computational methods are continuously being developed and refined to probe and reveal the atomistic details of protein folding dynamics and mechanisms. Herein, we provide a concise review of recent developments in spectroscopic studies of protein folding, with a focus on new triggering and probing methods. In particular, we describe several laser-based techniques for triggering protein folding/unfolding on the picosecond and/or nanosecond timescales and various linear and nonlinear spectroscopic techniques for interrogating protein conformations, conformational transitions, and dynamics.
Copyright © 2011 The Protein Society.

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Year:  2011        PMID: 22109973      PMCID: PMC3324760          DOI: 10.1002/pro.2006

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  149 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.  Fluorescence correlation spectroscopy of fast chain dynamics within denatured protein L.

Authors:  Eilon Sherman; Gilad Haran
Journal:  Chemphyschem       Date:  2011-01-26       Impact factor: 3.102

3.  Studies of peptides forming 3(10)- and alpha-helices and beta-bend ribbon structures in organic solution and in model biomembranes by Fourier transform infrared spectroscopy.

Authors:  D F Kennedy; M Crisma; C Toniolo; D Chapman
Journal:  Biochemistry       Date:  1991-07-02       Impact factor: 3.162

4.  Alpha-helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy.

Authors:  Jens Bredenbeck; Jan Helbing; Janet R Kumita; G Andrew Woolley; Peter Hamm
Journal:  Proc Natl Acad Sci U S A       Date:  2005-02-07       Impact factor: 11.205

5.  Picosecond dynamics of a membrane protein revealed by 2D IR.

Authors:  Prabuddha Mukherjee; Itamar Kass; Isaiah T Arkin; Isaiah Arkin; Martin T Zanni
Journal:  Proc Natl Acad Sci U S A       Date:  2006-02-27       Impact factor: 11.205

6.  Transient two-dimensional IR spectrometer for probing nanosecond temperature-jump kinetics.

Authors:  Hoi Sung Chung; Munira Khalil; Adam W Smith; Andrei Tokmakoff
Journal:  Rev Sci Instrum       Date:  2007-06       Impact factor: 1.523

7.  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

8.  Conformations of N-acetyl-L-prolinamide by two-dimensional infrared spectroscopy.

Authors:  Soohwan Sul; Denis Karaiskaj; Ying Jiang; Nien-Hui Ge
Journal:  J Phys Chem B       Date:  2006-10-12       Impact factor: 2.991

9.  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

10.  Residue-specific, real-time characterization of lag-phase species and fibril growth during amyloid formation: a combined fluorescence and IR study of p-cyanophenylalanine analogs of islet amyloid polypeptide.

Authors:  Peter Marek; Sudipta Mukherjee; Martin T Zanni; Daniel P Raleigh
Journal:  J Mol Biol       Date:  2010-06-01       Impact factor: 5.469

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  35 in total

1.  Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function.

Authors:  Beatrice N Markiewicz; Robert M Culik; Feng Gai
Journal:  Sci China Chem       Date:  2014-12       Impact factor: 9.445

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.  Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling.

Authors:  Carlos R Baiz; Andrei Tokmakoff
Journal:  Biophys J       Date:  2015-04-07       Impact factor: 4.033

4.  Dual time-resolved temperature-jump fluorescence and infrared spectroscopy for the study of fast protein dynamics.

Authors:  Caitlin M Davis; Michael J Reddish; R Brian Dyer
Journal:  Spectrochim Acta A Mol Biomol Spectrosc       Date:  2017-02-02       Impact factor: 4.098

5.  α-helix to β-hairpin transition of human amylin monomer.

Authors:  Sadanand Singh; Chi-cheng Chiu; Allam S Reddy; Juan J de Pablo
Journal:  J Chem Phys       Date:  2013-04-21       Impact factor: 3.488

6.  A molecular interpretation of 2D IR protein folding experiments with Markov state models.

Authors:  Carlos R Baiz; Yu-Shan Lin; Chunte Sam Peng; Kyle A Beauchamp; Vincent A Voelz; Vijay S Pande; Andrei Tokmakoff
Journal:  Biophys J       Date:  2014-03-18       Impact factor: 4.033

Review 7.  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

8.  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

9.  Coordination to lanthanide ions distorts binding site conformation in calmodulin.

Authors:  Sean C Edington; Andrea Gonzalez; Thomas R Middendorf; D Brent Halling; Richard W Aldrich; Carlos R Baiz
Journal:  Proc Natl Acad Sci U S A       Date:  2018-03-15       Impact factor: 11.205

10.  Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

Authors:  Hossein Fazelinia; Ming Xu; Hong Cheng; Heinrich Roder
Journal:  J Am Chem Soc       Date:  2013-12-31       Impact factor: 15.419

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