Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

Maxim B. Prigozhin, Yi Zhang, Klaus Schulten, Martin Gruebele, Taras V. Pogorelov

Research output: Contribution to journalArticle

Abstract

As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ 6 – 85 ) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the non-perturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α 3 D)], whose drying and core formation proceed in concert, λ 6 – 85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

Original languageEnglish (US)
Pages (from-to)5356-5361
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number12
DOIs
StatePublished - Jan 1 2019

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Protein Folding
Dehydration
Pressure
Molecular Dynamics Simulation
Fluorescent Dyes
Proteins

Keywords

  • Molecular dynamics simulation
  • Pressure jump
  • Protein solvation dynamics

ASJC Scopus subject areas

  • General

Cite this

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title = "Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics",
abstract = "As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three {\~A}Ž{\^A}»-repressor fragment ({\~A}Ž{\^A}» 6 {\~A}¢{\^a}‚¬{\^a}€œ 85 ) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix{\~A}¢{\^a}‚¬{\^a}€œhelix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the non-perturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the {\~A}Ž{\^A}±-helix 1{\~A}¢{\^a}‚¬{\^a}€œ3 pair distance displays a slower characteristic time scale than the 1{\~A}¢{\^a}‚¬{\^a}€œ2 or 3{\~A}¢{\^a}‚¬{\^a}€œ2 pair distance. To see whether slow packing of {\~A}Ž{\^A}±-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1{\~A}¢{\^a}‚¬{\^a}€œ3 contact formation indeed is much slower than when monitored by 1{\~A}¢{\^a}‚¬{\^a}€œ2 or 3{\~A}¢{\^a}‚¬{\^a}€œ2 contact formation. Unlike the case of the two-state folder [three{\~A}¢{\^a}‚¬{\^a}€œ{\~A}Ž{\^A}±-helix bundle ({\~A}Ž{\^A}± 3 D)], whose drying and core formation proceed in concert, {\~A}Ž{\^A}» 6 {\~A}¢{\^a}‚¬{\^a}€œ 85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non{\~A}¢{\^a}‚¬{\^a}€œtwo-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.",
keywords = "Molecular dynamics simulation, Pressure jump, Protein solvation dynamics",
author = "Prigozhin, {Maxim B.} and Yi Zhang and Klaus Schulten and Martin Gruebele and Pogorelov, {Taras V.}",
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T1 - Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics

AU - Prigozhin, Maxim B.

AU - Zhang, Yi

AU - Schulten, Klaus

AU - Gruebele, Martin

AU - Pogorelov, Taras V.

PY - 2019/1/1

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N2 - As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ 6 – 85 ) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the non-perturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α 3 D)], whose drying and core formation proceed in concert, λ 6 – 85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

AB - As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study pressure-drop refolding of three λ-repressor fragment (λ 6 – 85 ) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the non-perturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α 3 D)], whose drying and core formation proceed in concert, λ 6 – 85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.

KW - Molecular dynamics simulation

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