Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage

Abaskharon, Rachel M.; Culik, Robert M.; Woolley, G. Andrew; Gai, Feng

doi:10.1021/jz502654q

Cited by 13 publications

(18 citation statements)

References 74 publications

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“…1). Temporal resolution and structural sensitivity were achieved using transient-infrared (IR) measurements after a laser-induced temperature-jump (T-jump) (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33) in the amide I 0 spectral region, which is a sensitive probe of the backbone conformation (34)(35)(36)(37). Combined analysis of our steady-state ultraviolet circular dichroism (UV CD) and T-jump transient-IR measurements allows a detailed study of the folding and unfolding kinetics.…”

Section: Introductionmentioning

confidence: 99%

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α -Helical Stability and Folding Kinetics

Meuzelaar

Vreede

Woutersen

2016

Biophysical Journal

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Using a combination of ultraviolet circular dichroism, temperature-jump transient-infrared spectroscopy, and molecular dynamics simulations, we investigate the effect of salt bridges between different types of charged amino-acid residue pairs on α-helix folding. We determine the stability and the folding and unfolding rates of 12 alanine-based α-helical peptides, each of which has a nearly identical composition containing three pairs of positively and negatively charged residues (either Glu(-)/Arg(+), Asp(-)/Arg(+), or Glu(-)/Lys(+)). Within each set of peptides, the distance and order of the oppositely charged residues in the peptide sequence differ, such that they have different capabilities of forming salt bridges. Our results indicate that stabilizing salt bridges (in which the interacting residues are spaced and ordered such that they favor helix formation) speed up α-helix formation by up to 50% and slow down the unfolding of the α-helix, whereas salt bridges with an unfavorable geometry have the opposite effect. Comparing the peptides with different types of charge pairs, we observe that salt bridges between side chains of Glu(-) and Arg(+) are most favorable for the speed of folding, probably because of the larger conformational space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+). We speculate that the observed impact of salt bridges on the folding kinetics might explain why some proteins contain salt bridges that do not stabilize the final, folded conformation.

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Section: Introductionmentioning

confidence: 99%

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α -Helical Stability and Folding Kinetics

Meuzelaar

Vreede

Woutersen

2016

Biophysical Journal

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“…Abaskharon et al . 82 tested this hypothesis using a photoactivatable azobenzene cross-linker and the 10b variant of the mini-protein Trp-cage. As the single α-helix in Trp-cage is formed in the TS, 83-86 the azobenzene cross-linker, when appropriately attached to this α-helix (i.e., between residues 1 and 8), can initiate α-helix formation and also impose a geometric constraint on the TS upon photoswitching the azobenzene moiety from the trans to cis conformation.…”

Section: Results and Disscussionmentioning

confidence: 99%

Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function

2016

Self Cite

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While folding or performing functions, a protein can sample a rich set of conformational space. However, experimentally capturing all of the important motions with sufficient detail to allow a mechanistic description of their dynamics is nontrivial since such conformational events often occur over a wide range of time and length scales. Therefore, many methods have been employed to assess protein conformational dynamics and, depending on the nature of the conformational transition in question, some may be more advantageous than others. Herein, we describe our recent efforts, and also those of others, wherever appropriate, to use infrared- and fluorescence-based techniques to interrogate protein folding and functional dynamics. Specifically, we focus on discussing how to use extrinsic spectroscopic probes to enhance the structural resolution of these techniques and how to exploit various cross-linking strategies to acquire dynamic and mechanistic information that was previously difficult to attain.

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“…This has been nicely demonstrated by the works of Zinth and coworkers (43), Hamm and co-workers (44,45), and Kliger and co-workers (46). More recently, Abaskharon et al used an azobenzene cross-linker to manipulate the rigidity of the transition state structure and hence the attempt frequency of a protein folding reaction (47). Specifically, they strategically placed an azobenzene moiety in the a-helix of the miniprotein Trp-cage, which was previously shown to be involved in the major folding transition state.…”

Section: Ensemble Spectroscopic Studiesmentioning

confidence: 88%

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

Abaskharon

Gai

2016

Biophysical Journal

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As judged by a single publication metric, the activity in the protein folding field has been declining over the past 5 years, after enjoying a decade-long growth. Does this development indicate that the field is sunsetting or is this decline only temporary? Upon surveying a small territory of its landscape, we find that the protein folding field is still quite active and many important findings have emerged from recent experimental studies. However, it is also clear that only continued development of new techniques and methods, especially those enabling dissection of the fine details and features of the protein folding energy landscape, will fuel this old field to move forward.

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Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage

Cited by 13 publications

References 74 publications

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α -Helical Stability and Folding Kinetics

Influence of Glu/Arg, Asp/Arg, and Glu/Lys Salt Bridges on α -Helical Stability and Folding Kinetics

Infrared and Fluorescence Assessment of Protein Dynamics: From Folding to Function

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

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