Fast Events in Protein Folding:  Relaxation Dynamics and Structure of the I Form of Apomyoglobin

Gilmanshin, Rudolf; Williams, Sharon; Callender, Robert; Woodruff, William H.; Dyer, R. Brian

doi:10.1021/bi970634r

Cited by 67 publications

(72 citation statements)

References 32 publications

(60 reference statements)

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“…33,34,[46][47][48][49] However, the solubility problem severely hinders the application of the method to forward folding dynamics. We adopted the strategy developed by Wright and co-workers and increased the solubility of apoMb by adding 10% ethanol, 27,40 and were successful in characterizing its entire folding dynamics with a time resolution of 100 μs.…”

Section: Discussionmentioning

confidence: 99%

Solvation and Desolvation Dynamics in Apomyoglobin Folding Monitored by Time-resolved Infrared Spectroscopy

Nishiguchi¹,

Goto²,

Takahashi³

2007

Journal of Molecular Biology

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Section: Discussionmentioning

confidence: 99%

Solvation and Desolvation Dynamics in Apomyoglobin Folding Monitored by Time-resolved Infrared Spectroscopy

Nishiguchi¹,

Goto²,

Takahashi³

2007

Journal of Molecular Biology

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“…In the past few years, new fast experimental methods Burton et al, 1997;Callendar et al, 1999! have shown that proteins can fold at nearly diffusion-limited rates, on submillisecond time scales~Huang & Oas, 1995; Ballew et al, 1996aBallew et al, , 1996bPascher et al, 1996;Burton et al, 1997;Chan C-K et al, 1997; Gilmanshin et al, 1997aGilmanshin et al, , 1997bGilmanshin et al, , 1998!. Energy landscapes provide the language that can help describe folding events at any level, from the microscopic to the macroscopic.…”

Section: Ensemble Perspectivementioning

confidence: 99%

Polymer principles and protein folding

1999

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This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local fc propensities. The polymer perspective resolves two classic puzzles:~1! the Blind Watchmaker's Paradox that biological proteins could not have originated from random sequences, and~2! Levinthal's Paradox that the folded state of a protein cannot be found by random search. Both paradoxes are traditionally framed in terms of random unguided searches through vast spaces, and vastness is equated with impossibility. But both processes are partly guided. The searches are more akin to balls rolling down funnels than balls rolling aimlessly on flat surfaces. In both cases, the vastness of the search is largely irrelevant to the search time and success. These ideas are captured by energy and fitness landscapes. Energy landscapes give a language for bridging between microscopics and macroscopics, for relating folding kinetics to equilibrium fluctuations, and for developing new and faster computational search strategies. Keywords: new view; polymer; protein folding; statistical mechanicsThis paper describes a perspective on protein folding that derives in part from simple statistical mechanical and polymer models. As with any perspective, this one is a personal opinion, with all the limitations that implies. The first part of this paper explores the folding code.~1! Structure: How is the native structure encoded in the amino acid sequence?~2! Thermodynamics: Why is folding so cooperative?~3! Kinetics: What determines the speed and the ratelimiting steps of folding? Polymer modeling suggests that the folding code is more a solvation code and less a linear encoding of torsion angles along the peptide bond, even though the latter is not negligible. The second part explores the energy landscape perspective on folding kinetics. Polymer modeling suggests that the folding process more closely resembles balls rolling down bumpy funnels than balls rolling aimlessly on flat surfaces or rolling single file along identical trajectories.

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“…The amide IЈ band of polypeptides is due mainly to the amide CAO stretch vibration. Its sensitivity to conformation and conformational change is well documented (22)(23)(24)(25)(26). Although the protein amide IЈ band has been used extensively for conformation analysis, it is often difficult to differentiate signals arising from different residues because the transitions are broadened from both inhomogeneous and homogeneous mechanisms.…”

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confidence: 99%

Helix formation via conformation diffusion search

Huang

Getahun

Zhu

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

223

342

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The helix-coil transition kinetics of an ␣-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with 13 C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study.T he helix-coil transition represents the simplest scenario in protein folding (1-9), yet the details of its kinetics are not understood fully. The classical helix-coil transition theory describes the mechanism of helix formation as a sequence of events, starting from a so-called nucleation step where the first helical hydrogen bond, formed between the amide carbonyl of residue i and the amide hydrogen of residue iϩ4, is generated. The subsequent steps involve helix elongation by adding an extra hydrogen bond at either end of the preexisting helical turns. It has been argued that the nucleation process encounters the largest free energy barrier during the course of helix formation because three residues concomitantly lose their conformational entropy, whereas the propagation steps are energetically favorable because only one residue loses conformational entropy that is balanced by the energy generated from the formation of one extra hydrogen bond. Provided that the nucleation barrier is large enough (compared with those encountered by the propagation steps), a two-state scenario as well as transition-state theory remains effective to explain the dynamics of helix formation. Although recent experiments on the helix-coil transition employing laser-induced temperature-jump (T-jump) method (10-13) have shown that single exponential kinetics, which are characteristic of a two-state system, seem to be adequate to describe the transition between helix-containing and nonhelixcontaining conformations, other studies involving theory and molecular dynamics (MD) simulations have suggested that the helix-coil transition may not follow first-order kinetics (14,15). Another question that is also under debate involves the rate of the nucleation process. The T-jump data of infrared (10), fluorescence (11,12), and Raman (13), as well as results from an NMR experiment (16) all suggest that the nucleation step takes place on a submicrosecond time scale, whereas a stopped-flow CD study (17) indicates that the nucleation process may be much slower, on millisecond time scales.Recently, a new view of protein folding, based on statistical mechanical models of protein-like lattice or off-lattice polymers, has gained popularity in explaining protein folding dynamics, especially inhomogeneous folding kinetics. This new view describes protein folding as parallel, diffusion-like m...

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Fast Events in Protein Folding: Relaxation Dynamics and Structure of the I Form of Apomyoglobin

Cited by 67 publications

References 32 publications

Solvation and Desolvation Dynamics in Apomyoglobin Folding Monitored by Time-resolved Infrared Spectroscopy

Solvation and Desolvation Dynamics in Apomyoglobin Folding Monitored by Time-resolved Infrared Spectroscopy

Polymer principles and protein folding

Helix formation via conformation diffusion search

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