1
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Scaletti C, Russell PPS, Hebel KJ, Rickard MM, Boob M, Danksagmüller F, Taylor SA, Pogorelov TV, Gruebele M. Hydrogen bonding heterogeneity correlates with protein folding transition state passage time as revealed by data sonification. Proc Natl Acad Sci U S A 2024; 121:e2319094121. [PMID: 38768341 PMCID: PMC11145292 DOI: 10.1073/pnas.2319094121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
Protein-protein and protein-water hydrogen bonding interactions play essential roles in the way a protein passes through the transition state during folding or unfolding, but the large number of these interactions in molecular dynamics (MD) simulations makes them difficult to analyze. Here, we introduce a state space representation and associated "rarity" measure to identify and quantify transition state passage (transit) events. Applying this representation to a long MD simulation trajectory that captured multiple folding and unfolding events of the GTT WW domain, a small protein often used as a model for the folding process, we identified three transition categories: Highway (faster), Meander (slower), and Ambiguous (intermediate). We developed data sonification and visualization tools to analyze hydrogen bond dynamics before, during, and after these transition events. By means of these tools, we were able to identify characteristic hydrogen bonding patterns associated with "Highway" versus "Meander" versus "Ambiguous" transitions and to design algorithms that can identify these same folding pathways and critical protein-water interactions directly from the data. Highly cooperative hydrogen bonding can either slow down or speed up transit. Furthermore, an analysis of protein-water hydrogen bond dynamics at the surface of WW domain shows an increase in hydrogen bond lifetime from folded to unfolded conformations with Ambiguous transitions as an outlier. In summary, hydrogen bond dynamics provide a direct window into the heterogeneity of transits, which can vary widely in duration (by a factor of 10) due to a complex energy landscape.
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Affiliation(s)
| | | | | | - Meredith M. Rickard
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Mayank Boob
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | | | - Stephen A. Taylor
- School of Music, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Taras V. Pogorelov
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- School of Chemical Sciences, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
- National Center for Supercomputer Applications, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL61801
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2
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Russell PPS, Rickard MM, Boob M, Gruebele M, Pogorelov TV. In silico protein dynamics in the human cytoplasm: Partial folding, misfolding, fold switching, and non-native interactions. Protein Sci 2023; 32:e4790. [PMID: 37774143 PMCID: PMC10578126 DOI: 10.1002/pro.4790] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/10/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
We examine the influence of cellular interactions in all-atom models of a section of the Homo sapiens cytoplasm on the early folding events of the three-helix bundle protein B (PB). While genetically engineered PB is known to fold in dilute water box simulations in three microseconds, the three initially unfolded PB copies in our two cytoplasm models using a similar force field did not reach the native state during 30-microsecond simulations. We did however capture the formation of all three helices in a compact native-like topology. Folding in vivo is delayed because intramolecular contact formation within PB is in direct competition with intermolecular contacts between PB and surrounding macromolecules. In extreme cases, intermolecular beta-sheets are formed. Interactions with other macromolecules are also observed to promote structure formation, for example when a PB helix in our simulations is shielded from solvent by macromolecular crowding. Sticking and crowding in our models initiate sampling of helix/sheet structural plasticity of PB. Relatedly, in past in vitro experiments, similar GA domains were shown to switch between two different folds. Finally, we also observed that stickiness between PB and the cellular environment can be modulated in our simulations through the reduction in protein hydrophobicity when we reversed PB back to the wild-type sequence. This study demonstrates that even fast-folding proteins can get stuck in non-native states in the cell, making them useful models for protein-chaperone interactions and early stages of aggregate formation relevant to cellular disease.
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Affiliation(s)
| | - Meredith M. Rickard
- Department of ChemistryUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Mayank Boob
- Center for Biophysics and Quantitative BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Martin Gruebele
- Department of ChemistryUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Biophysics and Quantitative BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Department of PhysicsUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
| | - Taras V. Pogorelov
- Department of ChemistryUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Biophysics and Quantitative BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- National Center for Supercomputing ApplicationsUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
- School of Chemical SciencesUniversity of Illinois Urbana‐ChampaignUrbanaIllinoisUSA
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3
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Chaudhari AS, Chatterjee A, Domingos CAO, Andrikopoulos PC, Liu Y, Andersson I, Schneider B, Lórenz-Fonfría VA, Fuertes G. Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222. Protein Sci 2023; 32:e4590. [PMID: 36764820 PMCID: PMC10019195 DOI: 10.1002/pro.4590] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Photoreceptors containing the light-oxygen-voltage (LOV) domain elicit biological responses upon excitation of their flavin mononucleotide (FMN) chromophore by blue light. The mechanism and kinetics of dark-state recovery are not well understood. Here we incorporated the non-canonical amino acid p-cyanophenylalanine (CNF) by genetic code expansion technology at forty-five positions of the bacterial transcription factor EL222. Screening of light-induced changes in infrared (IR) absorption frequency, electric field and hydration of the nitrile groups identified residues CNF31 and CNF35 as reporters of monomer/oligomer and caged/decaged equilibria, respectively. Time-resolved multi-probe UV/Visible and IR spectroscopy experiments of the lit-to-dark transition revealed four dynamical events. Predominantly, rearrangements around the A'α helix interface (CNF31 and CNF35) precede FMN-cysteinyl adduct scission, folding of α-helices (amide bands), and relaxation of residue CNF151. This study illustrates the importance of characterizing all parts of a protein and suggests a key role for the N-terminal A'α extension of the LOV domain in controlling EL222 photocycle length. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Aditya S Chaudhari
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Aditi Chatterjee
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Catarina A O Domingos
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Escola Superior de Tecnologia do Barreiro, Instituto Politécnico de Setúbal, Lavradio, Portugal
| | | | - Yingliang Liu
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Inger Andersson
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
| | | | - Gustavo Fuertes
- Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic
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4
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Threading single proteins through pores to compare their energy landscapes. Proc Natl Acad Sci U S A 2022; 119:e2202779119. [PMID: 36122213 PMCID: PMC9522335 DOI: 10.1073/pnas.2202779119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Protein function correlates with its structural dynamics. While theoretical approaches to studying protein energy landscapes are well developed, experimental methods that enable probing these landscapes of proteins remain challenging. We used solid-state nanopores to study the translocation behavior of three mutants of a helix bundle protein and quantified the number of energetically accessible conformational states for each mutant. We found that a slower-folding mutant with access to more conformational states translocates faster than a faster-folding mutant with a smaller number of accessible states, suggesting that ease of folding and ease of translocation are at odds in this case. Translocation of proteins is correlated with structural fluctuations that access conformational states higher in free energy than the folded state. We use electric fields at the solid-state nanopore to control the relative free energy and occupancy of different protein conformational states at the single-molecule level. The change in occupancy of different protein conformations as a function of electric field gives rise to shifts in the measured distributions of ionic current blockades and residence times. We probe the statistics of the ionic current blockades and residence times for three mutants of the λ-repressor family in order to determine the number of accessible conformational states of each mutant and evaluate the ruggedness of their free energy landscapes. Translocation becomes faster at higher electric fields when additional flexible conformations are available for threading through the pore. At the same time, folding rates are not correlated with ease of translocation; a slow-folding mutant with a low-lying intermediate state translocates faster than a faster-folding two-state mutant. Such behavior allows us to distinguish among protein mutants by selecting for the degree of current blockade and residence time at the pore. Based on these findings, we present a simple free energy model that explains the complementary relationship between folding equilibrium constants and translocation rates.
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5
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Li M, Razumtcev A, Yang R, Liu Y, Rong J, Geiger AC, Blanchard R, Pfluegl C, Taylor LS, Simpson GJ. Fluorescence-Detected Mid-Infrared Photothermal Microscopy. J Am Chem Soc 2021; 143:10809-10815. [PMID: 34270255 DOI: 10.1021/jacs.1c03269] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We demonstrate instrumentation and methods to enable fluorescence-detected photothermal infrared (F-PTIR) microscopy and then demonstrate the utility of F-PTIR to characterize the composition within phase-separated domains of model amorphous solid dispersions (ASDs) induced by water sorption. In F-PTIR, temperature-dependent changes in fluorescence quantum efficiency are shown to sensitively report on highly localized absorption of mid-infrared radiation. The spatial resolution with which infrared spectroscopy can be performed is dictated by fluorescence microscopy, rather than the infrared wavelength. Intrinsic ultraviolet autofluorescence of tryptophan and protein microparticles enabled label-free F-PTIR microscopy. Following proof of concept F-PTIR demonstration on model systems of polyethylene glycol (PEG) and silica gel, F-PTIR enabled the characterization of chemical composition within inhomogeneous ritonavir/polyvinylpyrrolidone-vinyl acetate (PVPVA) amorphous dispersions. Phase separation is implicated in the observation of critical behaviors in ASD dissolution kinetics, with the results of F-PTIR supporting the formation of phase-separated drug-rich domains upon water sorption in spin-cast films.
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Affiliation(s)
- Minghe Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Aleksandr Razumtcev
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ruochen Yang
- Physical and Industrial Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Youlin Liu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jiayue Rong
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Andreas C Geiger
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Romain Blanchard
- Pendar Technologies, 30 Spinelli Pl, Cambridge, Massachusetts 02138, United States
| | - Christian Pfluegl
- Pendar Technologies, 30 Spinelli Pl, Cambridge, Massachusetts 02138, United States
| | - Lynne S Taylor
- Physical and Industrial Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Garth J Simpson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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6
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Cai K, Zheng X, Hou Y, Chen F, Yan G, Zhuang D. Deciphering the structural preference encoded in amide-I vibrations of lysine dipeptide in gas phase and in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 247:119066. [PMID: 33091736 DOI: 10.1016/j.saa.2020.119066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
Protein's biological function is critically associated with its structural feature, which is encoded in its amino acid sequence. For evaluation of conformational fluctuation and folding mechanism, DFT calculations were performed on the model compound - lysine dipeptide (LYSD) in gas phase to demonstrate the correlation between amide-I vibrations and secondary structure. Molecular dynamics simulations were carried out for the structural dynamics of LYSD in aqueous solution. The results show that LYSD tends form C7eq, C5, β, PPII and α conformations in the gas phase and primarily presented PPII and α conformations in aqueous solution. The obtained amide-I vibrational frequencies of LYSD conformers were assigned, thus build the correlations between amide-I probes and secondary structure of LYSD. These results provide theoretical insights into the structural feature of LYSD through amide-I vibrations, and would shed light on site specific structural prediction of polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Yanjun Hou
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
| | - Feng Chen
- Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China
| | - Guiyang Yan
- Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Fujian Province University, Ningde 352100, China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou 350007, China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen 361005, China
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7
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Fluorine induced conformational switching and modulation in photophysical properties of 7-fluorotryptophan: Spectroscopic, quantum chemical calculation and molecular dynamics simulation studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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8
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Cai K, Liu J, Liu Y, Chen F, Yan G, Lin H. Application of a transparent window vibrational probe (azido probe) to the structural dynamics of model dipeptides and amyloid β-peptide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117681. [PMID: 31685425 DOI: 10.1016/j.saa.2019.117681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/02/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
The azido asymmetric stretching motion is widely used for the elucidation of the intrinsic conformational preference and folding mechanism of protein since it has strong vibrational absorbance in the spectral transparent windows. However, the possible secondary structural disturbance induced by the insertion of azido group in the side chain of polypeptides should be carefully evaluated. Here, DFT calculation and enhanced sampling method were employed for model dipeptides with or without azido substitution, and the outcome results show that the lower potential energy basins of isolated model dipeptides are consistent with the preferred structural distributions of model dipeptides in aqueous solution. The azido asymmetric stretching frequency shows its sensitivity to the backbone configurations just like amide-I vibration does, and the azido vibration exhibits great potential as a structural reporter in the transparent window. For the evaluation of the application of azido group in biologically related system, the structural dynamics of Aβ37-42 and N3-Aβ37-42 fragments and the self-assemble process of their protofiliments in aqueous solution were demonstrated. The outcome results show that the structural fluctuations of Aβ37-42 and its protofilament in aqueous solution are quite similar with or without azido substitution, and the dewetting transitions of Aβ37-42 and N3-Aβ37-42 β-sheet layers are both complete within 30 ns and assemble into stable protofilaments. Therefore, the azido asymmetric vibrational motion is a minimally invasive structural probe and would not introduce much disturbance to the structural dynamics of polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China.
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Ya'nan Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, 361005, Fujian, PR China
| | - Feng Chen
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Guiyang Yan
- Fujian Province University Key Laboratory of Green Energy and Environment Catalysis, Ningde Normal University, Ningde, 352100, PR China
| | - Huiqiu Lin
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, Fujian, PR China
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9
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Fast pressure-jump all-atom simulations and experiments reveal site-specific protein dehydration-folding dynamics. Proc Natl Acad Sci U S A 2019; 116:5356-5361. [PMID: 30837309 DOI: 10.1073/pnas.1814927116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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 (λ6-85) 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 nonperturbative 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 (α3D)], whose drying and core formation proceed in concert, λ6-85 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.
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10
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Mittal S, Shukla D. Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments. J Phys Chem B 2018; 122:10793-10805. [DOI: 10.1021/acs.jpcb.8b07076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Davis CM, Zanetti-Polzi L, Gruebele M, Amadei A, Dyer RB, Daidone I. A quantitative connection of experimental and simulated folding landscapes by vibrational spectroscopy. Chem Sci 2018; 9:9002-9011. [PMID: 30647892 PMCID: PMC6301204 DOI: 10.1039/c8sc03786h] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/02/2018] [Indexed: 11/23/2022] Open
Abstract
We break the barrier between simulation and experiment by comparing identical computed and experimental infrared observables.
For small molecule reaction kinetics, computed reaction coordinates often mimic experimentally measured observables quite accurately. Although nowadays simulated and measured biomolecule kinetics can be compared on the same time scale, a gap between computed and experimental observables remains. Here we directly compared temperature-jump experiments and molecular dynamics simulations of protein folding dynamics using the same observable: the time-dependent infrared spectrum. We first measured the stability and folding kinetics of the fastest-folding β-protein, the GTT35 WW domain, using its structurally specific infrared spectrum. The relaxation dynamics of the peptide backbone, β-sheets, turn, and random coil were measured independently by probing the amide I′ region at different frequencies. Next, the amide I′ spectra along folding/unfolding molecular dynamics trajectories were simulated by accurate mixed quantum/classical calculations. The simulated time dependence and spectral amplitudes at the exact experimental probe frequencies provided relaxation and folding rates in agreement with experimental observations. The calculations validated by experiment yield direct structural evidence for a rate-limiting reaction step where an intermediate state with either the first or second hairpin is formed. We show how folding switches from a more homogeneous (apparent two-state) process at high temperature to a more heterogeneous process at low temperature, where different parts of the WW domain fold at different rates.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
| | - Martin Gruebele
- Department of Chemistry and Department of Physics , University of Illinois at Urbana-Champaign , IL 61801 , USA.,Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , IL 61801 , USA
| | - Andrea Amadei
- Department of Chemical and Technological Sciences , University of Rome "Tor Vergata" , 00133 Rome , Italy
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , GA 30322 , USA .
| | - Isabella Daidone
- Department of Physical and Chemical Sciences , University of L'Aquila , 67010 L'Aquila , Italy .
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12
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Davis CM, Gruebele M. Labeling for Quantitative Comparison of Imaging Measurements in Vitro and in Cells. Biochemistry 2018; 57:1929-1938. [PMID: 29546761 DOI: 10.1021/acs.biochem.8b00141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Qualitative imaging of biomolecular localization and distribution inside cells has revolutionized cell biology. Most of these powerful techniques require modifications to the target biomolecule. Over the past 10 years, these techniques have been extended to quantitative measurements, from in-cell protein folding rates to complex dissociation constants to RNA lifetimes. Such measurements can be affected even when a target molecule is just mildly perturbed by its labels. Here, the impact of labeling on protein (and RNA) structure, stability, and function in cells is discussed via practical examples from the recent literature. General guidelines for selecting and validating modification sites are provided to bring the best from cell biology and imaging to quantitative biophysical experiments inside cells.
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13
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Abaskharon RM, Gai F. Meandering Down the Energy Landscape of Protein Folding: Are We There Yet? Biophys J 2017; 110:1924-32. [PMID: 27166801 DOI: 10.1016/j.bpj.2016.03.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
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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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania; The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania.
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14
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Singh P, Chowdhury PK. Unravelling the Intricacy of the Crowded Environment through Tryptophan Quenching in Lysozyme. J Phys Chem B 2017; 121:4687-4699. [DOI: 10.1021/acs.jpcb.7b01055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Priyanka Singh
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K. Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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15
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Biophysical characterization of soluble Pseudomonas syringae ice nucleation protein InaZ fragments. Int J Biol Macromol 2017; 94:634-641. [DOI: 10.1016/j.ijbiomac.2016.10.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/21/2016] [Accepted: 10/18/2016] [Indexed: 11/22/2022]
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16
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Mori T, Saito S. Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity. J Phys Chem B 2016; 120:11683-11691. [DOI: 10.1021/acs.jpcb.6b08066] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshifumi Mori
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan
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Sukenik S, Pogorelov TV, Gruebele M. Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of λ(6-85) Folding. J Phys Chem Lett 2016; 7:1960-1965. [PMID: 27101436 DOI: 10.1021/acs.jpclett.6b00582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The process of protein folding is known to involve global motions in a cooperative affair; the structure of most of the protein sequences is gained or lost over a narrow range of temperature, denaturant, or pressure perturbations. At the same time, recent simulations and experiments reveal a complex structural landscape with a rich set of local motions and conformational changes. We couple experimental kinetic and thermodynamic measurements with specifically tailored analysis of simulation data to isolate local versus global folding probes. We find that local probes exhibit lower melting temperatures, smaller surface area changes, and faster kinetics compared to global ones. We also see that certain local probes of folding match the global behavior more closely than others. Our work highlights the importance of using multiple probes to fully characterize protein folding dynamics by theory and experiment.
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Affiliation(s)
- Shahar Sukenik
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Taras V Pogorelov
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Martin Gruebele
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
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18
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Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange. Proc Natl Acad Sci U S A 2016; 113:4747-52. [PMID: 27078098 DOI: 10.1073/pnas.1522500113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in a λYA variant that is suggested to be an incipient downhill folder having an extrapolated folding rate constant of 2 × 10(5) s(-1) and a stability of 7.4 kcal·mol(-1) at 298 K. At least one H bond on each of the three largest helices (α1, α3, and α4) breaks during a common unfolding event that reflects global denaturation. The use of HX enables us to both examine folding under highly stabilizing, native-like conditions and probe the pretransition state region for stable species without the need to initiate the folding reaction. The equivalence of the stability determined at zero and high denaturant indicates that any residual denatured state structure minimally affects the stability even under native conditions. Using our ψ analysis method along with mutational ϕ analysis, we find that the three aforementioned helices are all present in the folding transition state. Hence, the free energy surface has a sufficiently high barrier separating the denatured and native states that folding appears cooperative even under extremely stable and fast folding conditions.
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19
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Limited cooperativity in protein folding. Curr Opin Struct Biol 2016; 36:58-66. [DOI: 10.1016/j.sbi.2015.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/09/2015] [Indexed: 01/07/2023]
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Perez A, Morrone JA, Simmerling C, Dill KA. Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol 2016; 36:25-31. [PMID: 26773233 DOI: 10.1016/j.sbi.2015.12.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 11/18/2022]
Abstract
Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: first, to fold small proteins with free-energy methods without knowing substructures and second, to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years--which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information.
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Affiliation(s)
- Alberto Perez
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Joseph A Morrone
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States
| | - Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, United States; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, United States; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, United States.
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