1
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Töpfer K, Upadhyay M, Meuwly M. Quantitative molecular simulations. Phys Chem Chem Phys 2022; 24:12767-12786. [PMID: 35593769 PMCID: PMC9158373 DOI: 10.1039/d2cp01211a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022]
Abstract
All-atom simulations can provide molecular-level insights into the dynamics of gas-phase, condensed-phase and surface processes. One important requirement is a sufficiently realistic and detailed description of the underlying intermolecular interactions. The present perspective provides an overview of the present status of quantitative atomistic simulations from colleagues' and our own efforts for gas- and solution-phase processes and for the dynamics on surfaces. Particular attention is paid to direct comparison with experiment. An outlook discusses present challenges and future extensions to bring such dynamics simulations even closer to reality.
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Affiliation(s)
- Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Meenu Upadhyay
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.
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2
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Meuwly M. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?. J Phys Chem B 2022; 126:2155-2167. [PMID: 35286087 DOI: 10.1021/acs.jpcb.2c00212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic simulations using accurate energy functions can provide molecular-level insight into functional motions of molecules in the gas and in the condensed phase. This Perspective delineates the present status of the field from the efforts of others and some of our own work and discusses open questions and future prospects. The combination of physics-based long-range representations using multipolar charge distributions and kernel representations for the bonded interactions is shown to provide realistic models for the exploration of the infrared spectroscopy of molecules in solution. For reactions, empirical models connecting dedicated energy functions for the reactant and product states allow statistically meaningful sampling of conformational space whereas machine-learned energy functions are superior in accuracy. The future combination of physics-based models with machine-learning techniques and integration into all-purpose molecular simulation software provides a unique opportunity to bring such dynamics simulations closer to reality.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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3
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Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. J Phys Chem B 2021; 125:10928-10938. [PMID: 34559531 DOI: 10.1021/acs.jpcb.1c05423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution are characterized from molecular dynamics simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on a multipolar (MTP) representation of the electrostatics, and a semiempirical DFT method. For the 1D infrared spectra, the frequency splitting between the two amide-I groups is 10 cm-1 from the PC, 13 cm-1 from the MTP, and 47 cm-1 from self-consistent charge density functional tight-binding (SCC-DFTB) simulations, compared with 25 cm-1 from experiment. The frequency trajectory required for the frequency fluctuation correlation function (FFCF) is determined from individual normal mode (INM) and full normal mode (FNM) analyses of the amide-I vibrations. The spectroscopy, time-zero magnitude of the FFCF C(t = 0), and the static component Δ02 from simulations using MTP and analysis based on FNM are all consistent with experiments for (Ala)3. Contrary to this, for the analysis excluding mode-mode coupling (INM), the FFCF decays to zero too rapidly and for simulations with a PC-based force field, the Δ02 is too small by a factor of two compared with experiments. Simulations with SCC-DFTB agree better with experiment for these observables than those from PC-based simulations. The conformational ensemble sampled from simulations using PCs is consistent with the literature (including PII, β, αR, and αL), whereas that covered by the MTP-based simulations is dominated by PII with some contributions from β and αR. This agrees with and confirms recently reported Bayesian-refined populations based on 1D infrared experiments. FNM analysis together with a MTP representation provides a meaningful model to correctly describe the dynamics of hydrated trialanine.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Pierre-André Cazade
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Akshaya K Das
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Tristan Bereau
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel 4056, Switzerland.,Department of Chemistry, Brown University, Providence/RI 02912, United States
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4
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Orioli S, Larsen AH, Bottaro S, Lindorff-Larsen K. How to learn from inconsistencies: Integrating molecular simulations with experimental data. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:123-176. [PMID: 32145944 DOI: 10.1016/bs.pmbts.2019.12.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modeling tool to interpret experimental measurements, and to use experimental data to refine our biophysical models. Thus, explicit integration and synergy between molecular simulations and experiments is fundamental for furthering our understanding of biological processes. This is especially true in the case where discrepancies between measured and simulated observables emerge. In this chapter, we provide an overview of some of the core ideas behind methods that were developed to improve the consistency between experimental information and numerical predictions. We distinguish between situations where experiments are used to refine our understanding and models of specific systems, and situations where experiments are used more generally to refine transferable models. We discuss different philosophies and attempt to unify them in a single framework. Until now, such integration between experiments and simulations have mostly been applied to equilibrium data, and we discuss more recent developments aimed to analyze time-dependent or time-resolved data.
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Affiliation(s)
- Simone Orioli
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Haahr Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Atomistic Simulations Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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Feng CJ, Dhayalan B, Tokmakoff A. Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala. Biophys J 2019; 114:2820-2832. [PMID: 29925019 DOI: 10.1016/j.bpj.2018.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 10/28/2022] Open
Abstract
Characterizing ensembles of intrinsically disordered proteins is experimentally challenging because of the ill-conditioned nature of ensemble determination with limited data and the intrinsic fast dynamics of the conformational ensemble. Amide I two-dimensional infrared (2D IR) spectroscopy has picosecond time resolution to freeze structural ensembles as needed for probing disordered-protein ensembles and conformational dynamics. Also, developments in amide I computational spectroscopy now allow a quantitative and direct prediction of amide I spectra based on conformational distributions drawn from molecular dynamics simulations, providing a route to ensemble refinement against experimental spectra. We performed a Bayesian ensemble refinement method on Ala-Ala-Ala against isotope-edited Fourier-transform infrared spectroscopy and 2D IR spectroscopy and tested potential factors affecting the quality of ensemble refinements. We found that isotope-edited 2D IR spectroscopy provides a stringent constraint on Ala-Ala-Ala conformations and returns consistent conformational ensembles with the dominant ppII conformer across varying prior distributions from many molecular dynamics force fields and water models. The dominant factor influencing ensemble refinements is the systematic frequency uncertainty from spectroscopic maps. However, the uncertainty of conformer populations can be significantly reduced by incorporating 2D IR spectra in addition to traditional Fourier-transform infrared spectra. Bayesian ensemble refinement against isotope-edited 2D IR spectroscopy thus provides a route to probe equilibrium-complex protein ensembles and potentially nonequilibrium conformational dynamics.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Balamurugan Dhayalan
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois.
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6
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Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques. Biomolecules 2019; 9:biom9080370. [PMID: 31416261 PMCID: PMC6723403 DOI: 10.3390/biom9080370] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/08/2019] [Accepted: 08/11/2019] [Indexed: 11/21/2022] Open
Abstract
With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’.
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7
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Lanza G, Chiacchio MA. Quantum Mechanics Study on Hydrophilic and Hydrophobic Interactions in the Trivaline-Water System. J Phys Chem B 2018; 122:4289-4298. [PMID: 29584432 DOI: 10.1021/acs.jpcb.8b00833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the aim to elucidate hydrophobic effects in the unfolded state of peptides, DFT-M062X computations on the Val3H+· nH2O ( n up to 22) clusters have been accomplished. As far as the main chain is concerned, four conformers with β-strand and/or polyproline type II conformations, PPII (indicated as β-β, β-PPII, PPII-β, and PPII-PPII), have been found by changing the ϕ and ψ angles. For bare peptide, the side chain (isopropyl) of each residue can independently take on three different orientations with negligible effects on energetics. The great isopropyl spatial separations in β-β and β-PPII conformers allow for the construction of synergic and extensive water-water and water-peptide H-bonding in the minimal hydration Val3H+·22H2O models without significant steric encumbrance. Conversely, due to the proximity of the isopropyl of the central residue with the other two, some restrictions in the water shell construction around the peptide become evident for the PPII-PPII conformer and the number of energetically accessible structures decreases. This is indicative of correlated motion involving isopropyls and backbone mediated by water molecules, the origin of the nearest neighbor effects. Comparing the thermodynamic data of Ala3H+·22H2O and Val3H+·22H2O, what emerges is that both hydration enthalpy and entropy drive the β-strand stability of the latter.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
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8
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Lanza G, Chiacchio MA. Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine. Chemphyschem 2017; 18:1586-1596. [PMID: 28371186 DOI: 10.1002/cphc.201700149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/11/2022]
Abstract
A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H2 O, Ala2 H+ ⋅18 H2 O, and Ala2 ⋅18 H2 O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, Catania, 95125, Italy
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9
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Bonomi M, Heller GT, Camilloni C, Vendruscolo M. Principles of protein structural ensemble determination. Curr Opin Struct Biol 2017; 42:106-116. [PMID: 28063280 DOI: 10.1016/j.sbi.2016.12.004] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/18/2016] [Accepted: 12/06/2016] [Indexed: 01/19/2023]
Abstract
The biological functions of protein molecules are intimately dependent on their conformational dynamics. This aspect is particularly evident for disordered proteins, which constitute perhaps one-third of the human proteome. Therefore, structural ensembles often offer more useful representations of proteins than individual conformations. Here, we describe how the well-established principles of protein structure determination should be extended to the case of protein structural ensembles determination. These principles concern primarily how to deal with conformationally heterogeneous states, and with experimental measurements that are averaged over such states and affected by a variety of errors. We first review the growing literature of recent methods that combine experimental and computational information to model structural ensembles, highlighting their similarities and differences. We then address some conceptual problems in the determination of structural ensembles and define future goals towards the establishment of objective criteria for the comparison, validation, visualization and dissemination of such ensembles.
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Affiliation(s)
| | | | - Carlo Camilloni
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, D-85747 Garching, Germany
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10
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Lanza G, Chiacchio MA. Effects of Hydration on the Zwitterion Trialanine Conformation by Electronic Structure Theory. J Phys Chem B 2016; 120:11705-11719. [DOI: 10.1021/acs.jpcb.6b08108] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Giuseppe Lanza
- Dipartimento
di Scienze del
Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Maria A. Chiacchio
- Dipartimento
di Scienze del
Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy
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11
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Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Lu Zhang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Zhijun Liu
- National Center for Protein Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; Shanghai China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Xu Zhang
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Maili Liu
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Xuhui Huang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
- Division of Biomedical Engineering; Center of Systems Biology and Human Health; Institute for Advance Study and School of Science; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
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12
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Feng Y, Zhang L, Wu S, Liu Z, Gao X, Zhang X, Liu M, Liu J, Huang X, Wang W. Conformational Dynamics of apo-GlnBP Revealed by Experimental and Computational Analysis. Angew Chem Int Ed Engl 2016; 55:13990-13994. [PMID: 27730716 DOI: 10.1002/anie.201606613] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/28/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Yitao Feng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Lu Zhang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Shaowen Wu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Zhijun Liu
- National Center for Protein Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; Shanghai China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST); Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division; Thuwal 23955 Saudi Arabia
| | - Xu Zhang
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Maili Liu
- Key Laboratory of Magnetic and Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics; Centre for Magnetic Resonance; Wuhan Institute of Physics and Mathematics; Chinese Academy of Sciences; Wuhan China
| | - Jianwei Liu
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
| | - Xuhui Huang
- Department of Chemistry; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
- Division of Biomedical Engineering; Center of Systems Biology and Human Health; Institute for Advance Study and School of Science; The Hong Kong University of Science and Technology; Clear Water Bay Kowloon Hong Kong
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Department of Chemistry, and Institutes of Biomedical Sciences; Fudan University; Shanghai P.R. China
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13
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Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput 2016; 11:325-31. [PMID: 25620895 PMCID: PMC4295808 DOI: 10.1021/ct5009125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 12/18/2022]
Abstract
![]()
Given
the demonstrated utility of coarse-grained modeling and simulations
approaches in studying protein structure and dynamics, developing
methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In
this work, we develop one such method that enables protein backbone
chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based
method, LARMORCα, predicts backbone chemical shifts
with comparable accuracy to some all-atom approaches. More importantly,
we demonstrate that LARMORCα predicted chemical shifts
are able to resolve native structure from decoy pools that contain
both native and non-native models, and so it is sensitive to protein
structure. As an application, we use LARMORCα to
characterize the transient state of the fast-folding protein gpW using
recently published NMR relaxation dispersion derived backbone chemical
shifts. The model we obtain is consistent with the previously proposed
model based on independent analysis of the chemical shift dispersion
pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational
substates to be identified by “parsing” trajectories
and ensembles generated using coarse-grained modeling and simulations.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA, Campbell BA, Brown RF, Guo C, Schrodt M, Liu YT, Elcock AH. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. J Chem Theory Comput 2016; 11:1315-29. [PMID: 26579777 DOI: 10.1021/ct5010966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. (3)J(HNHα) coupling constants and δ(Hα) chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average (3)J(HNHα) and δ(Hα) values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.
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Affiliation(s)
- Shuxiang Li
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | | | - Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Stephen L Siemonsma
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | | | - Isaac T Rockafellow
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Nguyet Anh Ngo
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Brady A Campbell
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Reid F Brown
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Chengxuan Guo
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Michael Schrodt
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Yu-Tsan Liu
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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15
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Brookes DH, Head-Gordon T. Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins. J Am Chem Soc 2016; 138:4530-8. [PMID: 26967199 DOI: 10.1021/jacs.6b00351] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We develop a Bayesian approach to determine the most probable structural ensemble model from candidate structures for intrinsically disordered proteins (IDPs) that takes full advantage of NMR chemical shifts and J-coupling data, their known errors and variances, and the quality of the theoretical back-calculation from structure to experimental observables. Our approach differs from previous formulations in the optimization of experimental and back-calculation nuisance parameters that are treated as random variables with known distributions, as opposed to structural or ensemble weight optimization or use of a reference ensemble. The resulting experimental inferential structure determination (EISD) method is size extensive with O(N) scaling, with N = number of structures, that allows for the rapid ranking of large ensemble data comprising tens of thousands of conformations. We apply the EISD approach on singular folded proteins and a corresponding set of ∼25 000 misfolded states to illustrate the problems that can arise using Boltzmann weighted priors. We then apply the EISD method to rank IDP ensembles most consistent with the NMR data and show that the primary error for ranking or creating good IDP ensembles resides in the poor back-calculation from structure to simulated experimental observable. We show that a reduction by a factor of 3 in the uncertainty of the back-calculation error can improve the discrimination among qualitatively different IDP ensembles for the amyloid-beta peptide.
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Affiliation(s)
- David H Brookes
- Department of Chemistry, ‡Department of Bioengineering, §Department of Chemical and Biomolecular Engineering, ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California , Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Department of Chemistry, ‡Department of Bioengineering, §Department of Chemical and Biomolecular Engineering, ∥Chemical Sciences Division, Lawrence Berkeley National Laboratory, University of California , Berkeley, California 94720, United States
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16
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Bastida A, Zúñiga J, Requena A, Miguel B, Candela ME, Soler MA. Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode. J Phys Chem B 2016; 120:348-57. [PMID: 26690744 DOI: 10.1021/acs.jpcb.5b09753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Beatriz Miguel
- Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena , 30203 Cartagena, Spain
| | | | - Miguel Angel Soler
- Department of Medical and Biological Sciences, University of Udine , 33100 Udine, Italy
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17
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Lanza G, Chiacchio MA. Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation. Phys Chem Chem Phys 2015; 17:17101-11. [DOI: 10.1039/c5cp00270b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco
- Università di Catania
- 95125 Catania
- Italy
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