1
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Tolokh IS, Folescu DE, Onufriev AV. Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. J Phys Chem B 2024; 128:5855-5873. [PMID: 38860842 PMCID: PMC11194828 DOI: 10.1021/acs.jpcb.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024]
Abstract
The current practical "workhorses" of the atomistic implicit solvation─the Poisson-Boltzmann (PB) and generalized Born (GB) models─face fundamental accuracy limitations. Here, we propose a computationally efficient implicit solvation framework, the Implicit Water Multipole GB (IWM-GB) model, that systematically incorporates the effects of multipole moments of water molecules in the first hydration shell of a solute, beyond the dipole water polarization already present at the PB/GB level. The framework explicitly accounts for coupling between polar and nonpolar contributions to the total solvation energy, which is missing from many implicit solvation models. An implementation of the framework, utilizing the GAFF force field and AM1-BCC atomic partial charges model, is parametrized and tested against the experimental hydration free energies of small molecules from the FreeSolv database. The resulting accuracy on the test set (RMSE ∼ 0.9 kcal/mol) is 12% better than that of the explicit solvation (TIP3P) treatment, which is orders of magnitude slower. We also find that the coupling between polar and nonpolar parts of the solvation free energy is essential to ensuring that several features of the IWM-GB model are physically meaningful, including the sign of the nonpolar contributions.
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Affiliation(s)
- Igor S. Tolokh
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Dan E. Folescu
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Mathematics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexey V. Onufriev
- Department
of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, United States
- Department
of Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia 24061, United States
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2
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Sari L, Bali S, Joachimiak LA, Lin MM. Hairpin trimer transition state of amyloid fibril. Nat Commun 2024; 15:2756. [PMID: 38553453 PMCID: PMC10980705 DOI: 10.1038/s41467-024-46446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Protein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.
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Affiliation(s)
- Levent Sari
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milo M Lin
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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3
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Coppa C, Bazzoli A, Barkhordari M, Contini A. Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models. J Chem Inf Model 2023; 63:3030-3042. [PMID: 37163419 DOI: 10.1021/acs.jcim.3c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.
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Affiliation(s)
- Crescenzo Coppa
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Andrea Bazzoli
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Maral Barkhordari
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
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4
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Arsiccio A, Liu X, Ganguly P, Buratto SK, Bowers MT, Shea JE. Effect of Cosolutes on the Aggregation of a Tau Fragment: A Combined Experimental and Simulation Approach. J Phys Chem B 2023; 127:4022-4031. [PMID: 37129599 DOI: 10.1021/acs.jpcb.3c00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The intrinsically disordered protein Tau represents the main component of neurofibrillary tangles that are a hallmark of Alzheimer's disease. A small fragment of Tau, known as paired helical filament 6 (PHF6), is considered to be important for the formation of the β-structure core of the fibrils. Here we study the aggregation of this fragment in the presence of different cosolutes, including urea, TMAO, sucrose and 2-hydroxypropyl-β-cyclodextrin (2-HPβCD), using both experiments and molecular dynamics simulations. A novel implicit solvation approach (MIST - Model with Implicit Solvation Thermodynamics) is used, where an energetic contribution based on the concept of transfer free energies describes the effect of the cosolutes. The simulation predictions are compared to thioflavin-T and atomic force microscopy results, and the good agreement observed confirms the predictive ability of the computational approach herein proposed. Both simulations and experiments indicate that PHF6 aggregation is inhibited in the presence of urea and 2-HPβCD, while TMAO and sucrose stabilize associated conformations. The remarkable ability of HPβCD to inhibit aggregation represents an extremely promising result for future applications, especially considering the widespread use of this molecule as a drug carrier to the brain and as a solubilizer/excipient in pharmaceutical formulations.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Xikun Liu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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5
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Lang EJM, Baker EG, Woolfson DN, Mulholland AJ. Generalized Born Implicit Solvent Models Do Not Reproduce Secondary Structures of De Novo Designed Glu/Lys Peptides. J Chem Theory Comput 2022; 18:4070-4076. [PMID: 35687842 PMCID: PMC9281390 DOI: 10.1021/acs.jctc.1c01172] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We test a range of
standard generalized Born (GB) models and protein
force fields for a set of five experimentally characterized, designed
peptides comprising alternating blocks of glutamate and lysine, which
have been shown to differ significantly in α-helical content.
Sixty-five combinations of force fields and GB models are evaluated
in >800 μs of molecular dynamics simulations. GB models generally
do not reproduce the experimentally observed α-helical content,
and none perform well for all five peptides. These results illustrate
that these models are not usefully predictive in this context. These
peptides provide a useful test set for simulation methods.
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Affiliation(s)
- Eric J M Lang
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Emily G Baker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K.,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K.,School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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6
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Savva L, Platts JA. Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein. J Biomol Struct Dyn 2022:1-16. [PMID: 35670576 DOI: 10.1080/07391102.2022.2082534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Cardiff, UK
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7
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Tian C, Kasavajhala K, Belfon KAA, Raguette L, Huang H, Migues AN, Bickel J, Wang Y, Pincay J, Wu Q, Simmerling C. ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. J Chem Theory Comput 2019; 16:528-552. [PMID: 31714766 DOI: 10.1021/acs.jctc.9b00591] [Citation(s) in RCA: 805] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.
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Affiliation(s)
- Chuan Tian
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Koushik Kasavajhala
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Kellon A A Belfon
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Lauren Raguette
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - He Huang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Angela N Migues
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - John Bickel
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Yuzhang Wang
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jorge Pincay
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Qin Wu
- Center for Functional Nanomaterials , Brookhaven National Laboratory , Upton , New York 11973 , United States
| | - Carlos Simmerling
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States.,Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States
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8
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Sanyal T, Mittal J, Shell MS. A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model. J Chem Phys 2019; 151:044111. [PMID: 31370551 PMCID: PMC6663515 DOI: 10.1063/1.5108761] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/24/2019] [Indexed: 12/21/2022] Open
Abstract
Coarse-grained (CG) protein models in the structural biology literature have improved over the years from being simple tools to understand general folding and aggregation driving forces to capturing detailed structures achieved by actual folding sequences. Here, we ask whether such models can be developed systematically from recent advances in bottom-up coarse-graining methods without relying on bioinformatic data (e.g., protein data bank statistics). We use relative entropy coarse-graining to develop a hybrid CG but Go¯-like CG peptide model, hypothesizing that the landscape of proteinlike folds is encoded by the backbone interactions, while the sidechain interactions define which of these structures globally minimizes the free energy in a unique native fold. To construct a model capable of capturing varied secondary structures, we use a new extended ensemble relative entropy method to coarse-grain based on multiple reference atomistic simulations of short polypeptides with varied α and β character. Subsequently, we assess the CG model as a putative protein backbone forcefield by combining it with sidechain interactions based on native contacts but not incorporating native distances explicitly, unlike standard Go¯ models. We test the model's ability to fold a range of proteins and find that it achieves high accuracy (∼2 Å root mean square deviation resolution for both short sequences and large globular proteins), suggesting the strong role that backbone conformational preferences play in defining the fold landscape. This model can be systematically extended to non-natural amino acids and nonprotein polymers and sets the stage for extensions to non-Go¯ models with sequence-specific sidechain interactions.
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Affiliation(s)
- Tanmoy Sanyal
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - M. Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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9
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Shimizu M, Kajikawa Y, Kuwajima K, Dobson CM, Okamoto Y. Determination of the structural ensemble of the molten globule state of a protein by computer simulations. Proteins 2019; 87:635-645. [PMID: 30958596 DOI: 10.1002/prot.25688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 02/20/2019] [Accepted: 04/04/2019] [Indexed: 11/08/2022]
Abstract
We have used computer simulations to investigate the structural nature of the molten globule (MG) state of canine milk lysozyme. To sample the conformational space efficiently, we performed replica-exchange umbrella sampling simulations with the radius of gyration as a reaction coordinate. We applied the Weighted Histogram Analysis Method to the trajectory of the simulations to obtain the potential of mean force, from which we identified representative structures corresponding to local minima in the free energy surface. The representative structures obtained in this way are in accord with the characteristics of the MG state reported previously by experimental studies. We conjecture that the MG state comprises a series of partially structured states undergoing relatively fast conformational interchange.
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Affiliation(s)
- Masahiro Shimizu
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yukihito Kajikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Kunihiro Kuwajima
- Department of Physics, Graduate School of Science, University of Tokyo, Tokyo, Japan.,School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul, Korea
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.,Information Technology Center, Nagoya University, Nagoya, Aichi, Japan.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan.,Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan.,JST-CREST, Nagoya, Aichi, Japan
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10
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Depta PN, Jandt U, Dosta M, Zeng AP, Heinrich S. Toward Multiscale Modeling of Proteins and Bioagglomerates: An Orientation-Sensitive Diffusion Model for the Integration of Molecular Dynamics and the Discrete Element Method. J Chem Inf Model 2019; 59:386-398. [PMID: 30550276 DOI: 10.1021/acs.jcim.8b00613] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most processes involved in biological and biotechnological systems spread over many scales in space and time. For example, the interaction of multiple enzymes in heterogeneous enzymatic agglomerates or clusters, necessary for efficient enzymatic conversion, is of high interest for research and enzyme engineering. In order to understand and predict their overall behavior and performance, it is important to describe these scales as completely as possible, known as multiscale modeling. While many different approaches have been presented in recent years, knowledge about protein formation and bioagglomeration at the micro scale is still very limited. In an attempt to address such systems, we propose a bottom- up multiscale modeling methodology, bridging the gaps between molecular dynamics (MD) with an explicit solvent and the larger scale discrete element method (DEM) using an implicit solvent and abstracting macromolecules (e.g., proteins) as objects with anisotropic properties. We term this approach the molecular discrete element method (MDEM). For this, we present an orientation-sensitive diffusion model for DEM, which describes the dynamics of anisotropic translational and rotational diffusion, while implicitly considering solvent molecules and enforcing a canonical ensemble. A general-purpose model and parametrization approach is presented, which can be used to simulate any process involving diffusion of discrete particles. Effects of temperature and viscosity changes can be considered, and guidance is provided concerning time step selection. This model is generally applicable and serves as a precondition to enforce the proper dynamics (i.e., diffusion characteristics and canonical ensemble, similar to a thermostat in MD) for the proposed multiscale modeling methodology with anisotropic properties. Thereby, it presents a first step toward modeling at the micro scale and is integral to enforcing dynamics of such systems and therefore extensively validated. As a next step, interaction models are to be defined and added to the presented model. In comparison to atomistic and coarse-grained (CG) MD, a speedup of 5-7 orders of magnitude can be achieved. The approach is demonstrated on multiple components of the pyruvate dehydrogenase enzyme complex, a multienzymatic machinery that involves very different types of enzymes and is of high value to further elucidate the mechanisms of bioagglomeration and metabolic channeling.
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11
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Nishikawa N, Sakae Y, Gouda T, Tsujimura Y, Okamoto Y. Structural Analysis of a Trimer of β 2-Microgloblin Fragment by Molecular Dynamics Simulations. Biophys J 2019; 116:781-790. [PMID: 30771855 DOI: 10.1016/j.bpj.2018.11.3143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 06/08/2018] [Accepted: 11/06/2018] [Indexed: 01/22/2023] Open
Abstract
A peptide β2-m21-31, which is a fragment from residue 21 to residue 31 of β2-microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of β2-m21-31. From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates.
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Affiliation(s)
- Naohiro Nishikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aichi, Japan
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Takuya Gouda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuichiro Tsujimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi, Japan; Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan; Information Technology Center, Nagoya University, Nagoya, Aichi, Japan; JST-CREST, Nagoya, Aichi, Japan.
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12
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Shao Q, Yang L, Zhu W. Selective enhanced sampling in dihedral energy facilitates overcoming the dihedral energy increase in protein folding and accelerates the searching for protein native structure. Phys Chem Chem Phys 2019; 21:10423-10435. [DOI: 10.1039/c9cp00615j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A dihedral-energy-based selective enhanced sampling method (D-SITSMD) is presented with improved capabilities for searching a protein's natively folded structure and for providing the underlying folding pathway.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences
- Beijing
- China
- Institute of Theoretical and Computational Chemistry
- College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center
| | - Weiliang Zhu
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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13
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Shao Q, Zhu W. Assessing AMBER force fields for protein folding in an implicit solvent. Phys Chem Chem Phys 2018; 20:7206-7216. [PMID: 29480910 DOI: 10.1039/c7cp08010g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulation implemented with a state-of-the-art protein force field and implicit solvent model is an attractive approach to investigate protein folding, one of the most perplexing problems in molecular biology. But how well can force fields developed independently of implicit solvent models work together in reproducing diverse protein native structures and measuring the corresponding folding thermodynamics is not always clear. In this work, we performed enhanced sampling MD simulations to assess the ability of six AMBER force fields (FF99SBildn, FF99SBnmr, FF12SB, FF14ipq, FF14SB, and FF14SBonlysc) as coupled with a recently improved pair-wise GB-Neck2 model in modeling the folding of two helical and two β-sheet peptides. Whilst most of the tested force fields can yield roughly similar features for equilibrium conformational ensembles and detailed folding free-energy profiles for short α-helical TC10b in an implicit solvent, the measured counterparts are significantly discrepant in the cases of larger or β-structured peptides (HP35, 1E0Q, and GTT). Additionally, the calculated folding/unfolding thermodynamic quantities can only partially match the experimental data. Although a combination of the force fields and GB-Neck2 implicit model able to describe all aspects of the folding transitions towards the native structures of all the considered peptides was not identified, we found that FF14SBonlysc coupled with the GB-Neck2 model seems to be a reasonably balanced combination to predict peptide folding preferences.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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14
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Huang H, Simmerling C. Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs. J Chem Theory Comput 2018; 14:5797-5814. [PMID: 30303377 DOI: 10.1021/acs.jctc.8b00413] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a pairwise and readily parallelizable SASA-based nonpolar solvation approach for protein simulations, inspired by our previous pairwise GB polar solvation model development. In this work, we developed a novel function to estimate the atomic and molecular SASAs of proteins, which results in comparable accuracy as the LCPO algorithm in reproducing numerical icosahedral-based SASA values. Implemented in Amber software and tested on consumer GPUs, our pwSASA method reasonably reproduces LCPO simulation results, but accelerates MD simulations up to 30 times compared to the LCPO implementation, which is greatly desirable for protein simulations facing sampling challenges. The value of incorporating the nonpolar term in implicit solvent simulations is explored on a peptide fragment containing the hydrophobic core of HP36 and evaluating thermal stability profiles of four small proteins.
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Affiliation(s)
- He Huang
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
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15
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Mironov V, Alexeev Y, Mulligan VK, Fedorov DG. A systematic study of minima in alanine dipeptide. J Comput Chem 2018; 40:297-309. [DOI: 10.1002/jcc.25589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/12/2018] [Accepted: 08/07/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Mironov
- Department of Chemistry Lomonosov Moscow State University Leninskie Gory 1/3, Moscow 119991 Russia
| | - Yuri Alexeev
- Argonne National Laboratory Computational Science Division Argonne Illinois 60439
| | - Vikram Khipple Mulligan
- Department of Biochemistry University of Washington, Institute for Protein Design Seattle Washington 98195
| | - Dmitri G. Fedorov
- CD‐FMat National Institute of Advanced Industrial Science and Technology Central 2, Umezono 1‐1‐1, Tsukuba 305‐8568 Japan
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16
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Jusot M, Stratmann D, Vaisset M, Chomilier J, Cortés J. Exhaustive Exploration of the Conformational Landscape of Small Cyclic Peptides Using a Robotics Approach. J Chem Inf Model 2018; 58:2355-2368. [DOI: 10.1021/acs.jcim.8b00375] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Maud Jusot
- Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Dirk Stratmann
- Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Marc Vaisset
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Jacques Chomilier
- Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, 75005 Paris, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
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17
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Slough DP, McHugh SM, Lin YS. Understanding and designing head-to-tail cyclic peptides. Biopolymers 2018; 109:e23113. [PMID: 29528114 PMCID: PMC6135719 DOI: 10.1002/bip.23113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/30/2023]
Abstract
Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges. In addition, we provide several future directions in the field of computational CP design to improve its accuracy, efficiency and applicability. These advances, combined with experimental techniques, shall ultimately provide a better understanding of these interesting molecules and a reliable working platform to rationally design CPs with desired characteristics.
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Affiliation(s)
| | | | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts, 02155, United States
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18
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Ilitchev AI, Giammona MJ, Olivas C, Claud SL, Lazar Cantrell KL, Wu C, Buratto SK, Bowers MT. Hetero-oligomeric Amyloid Assembly and Mechanism: Prion Fragment PrP(106-126) Catalyzes the Islet Amyloid Polypeptide β-Hairpin. J Am Chem Soc 2018; 140:9685-9695. [PMID: 29989407 DOI: 10.1021/jacs.8b05925] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein aggregation is typically attributed to the association of homologous amino acid sequences between monomers of the same protein. Coaggregation of heterogeneous peptide species can occur, however, and is implicated in the proliferation of seemingly unrelated protein diseases in the body. The prion protein fragment (PrP106-126) and human islet amyloid polypeptide (hIAPP) serve as an interesting model of nonhomologous protein assembly as they coaggregate, despite a lack of sequence homology. We have applied ion-mobility mass spectrometry, atomic force microscopy, circular dichroism, and high-level molecular modeling to elucidate this important assembly process. We found that the prion fragment not only forms pervasive hetero-oligomeric aggregates with hIAPP but also promotes the transition of hIAPP into its amyloidogenic β-hairpin conformation. Further, when PrP106-126 was combined with non-amyloidogenic rIAPP, the two formed nearly identical hetero-oligomers to those seen with hIAPP, despite rIAPP containing β-sheet breaking proline substitutions. Additionally, while rIAPP does not natively form the amyloidogenic β-hairpin structure, it did so in the presence of PrP106-126 and underwent a conformational transition to β-sheet in solution. We also find that PrP106-126 forms hetero-oligomers with the IAPP8-20 fragment but not with the "aggregation hot spot" IAPP20-29 fragment. PrP106-126 apparently induces IAPP into a β-hairpin structure within the PrP:IAPP heterodimer complex and then, through ligand exchange, catalytically creates the amyloidogenic β-hairpin dimer of IAPP in significantly greater abundance than IAPP does on its own. This is a new mechanistic model that provides a critical foundation for the detailed study of hetero-oligomerization and prion-like proliferation in amyloid systems.
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Affiliation(s)
- Alexandre I Ilitchev
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Maxwell J Giammona
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Carina Olivas
- Department of Chemistry and Biochemistry , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Sarah L Claud
- Department of Chemistry , Westmont College , Santa Barbara , California 93108 , United States
| | - Kristi L Lazar Cantrell
- Department of Chemistry , Westmont College , Santa Barbara , California 93108 , United States
| | - Chun Wu
- Department of Chemistry and Biochemistry , Rowan University , Glassboro , New Jersey 08028 , United States
| | - Steven K Buratto
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry , University of California , Santa Barbara , California 93106 , United States
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19
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Shao Q, Zhu W. The effects of implicit modeling of nonpolar solvation on protein folding simulations. Phys Chem Chem Phys 2018; 20:18410-18419. [PMID: 29946610 DOI: 10.1039/c8cp03156h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute molecules are treated separately, have been widely adopted for molecular dynamics simulation of protein folding. While the development of the implicit models is mainly focused on the methodological improvement and key parameter optimization for polar solvation, nonpolar solvation has been either ignored or described by a simplistic surface area (SA) model. In this work, we performed the folding simulations of multiple β-hairpin and α-helical proteins with varied surface tension coefficients embedded in the SA model to clearly demonstrate the effects of nonpolar solvation treated by a popular SA model on protein folding. The results indicate that the change in the surface tension coefficient does not alter the ability of implicit solvent simulations to reproduce a protein native structure but indeed controls the components of the equilibrium conformational ensemble and modifies the energetic characterization of the folding transition pathway. The suitably set surface tension coefficient can yield explicit solvent simulations and/or experimentally suggested folding mechanism of protein. In addition, the implicit treatment of both polar and nonpolar components of solvation free-energy contributes to the overestimation of the secondary structure in implicit solvent simulations.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
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20
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Ge Y, Voelz VA. Model Selection Using BICePs: A Bayesian Approach for Force Field Validation and Parameterization. J Phys Chem B 2018. [PMID: 29518328 DOI: 10.1021/acs.jpcb.7b11871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Bayesian Inference of Conformational Populations (BICePs) algorithm reconciles theoretical predictions of conformational state populations with sparse and/or noisy experimental measurements. Among its key advantages is its ability to perform objective model selection through a quantity we call the BICePs score, which reflects the integrated posterior evidence in favor of a given model, computed through free energy estimation methods. Here, we explore how the BICePs score can be used for force field validation and parametrization. Using a 2D lattice protein as a toy model, we demonstrate that BICePs is able to select the correct value of an interaction energy parameter given ensemble-averaged experimental distance measurements. We show that if conformational states are sufficiently fine-grained, the results are robust to experimental noise and measurement sparsity. Using these insights, we apply BICePs to perform force field evaluations for all-atom simulations of designed β-hairpin peptides against experimental NMR chemical shift measurements. These tests suggest that BICePs scores can be used for model selection in the context of all-atom simulations. We expect this approach to be particularly useful for the computational foldamer design as a tool for improving general-purpose force fields given sparse experimental measurements.
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Affiliation(s)
- Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
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21
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Shao Q, Zhu W. How Well Can Implicit Solvent Simulations Explore Folding Pathways? A Quantitative Analysis of α-Helix Bundle Proteins. J Chem Theory Comput 2017; 13:6177-6190. [DOI: 10.1021/acs.jctc.7b00726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qiang Shao
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of
Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, CAS Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University of
Chinese Academy of Sciences, Beijing 100049, China
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22
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Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics; Virginia Tech; Blacksburg VA USA
- Department of Computer Science; Virginia Tech; Blacksburg VA USA
- Center for Soft Matter and Biological Physics; Virginia Tech; Blacksburg VA USA
| | - Saeed Izadi
- Early Stage Pharmaceutical Development; Genentech Inc.; South San Francisco, CA USA
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23
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Nishikawa N, Sakae Y, Gouda T, Tsujimura Y, Okamoto Y. Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1359746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Naohiro Nishikawa
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
| | - Yoshitake Sakae
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Takuya Gouda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuichiro Tsujimura
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
- Information Technology Center, Nagoya University, Nagoya, Japan
- JST-CREST, Nagoya, Japan
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24
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Bucci R, Bonetti A, Clerici F, Contini A, Nava D, Pellegrino S, Tessaro D, Gelmi ML. Tandem Tetrahydroisoquinoline-4-carboxylic Acid/β-Alanine as a New Construct Able To Induce a Flexible Turn. Chemistry 2017; 23:10822-10831. [PMID: 28467649 DOI: 10.1002/chem.201701045] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Indexed: 12/21/2022]
Abstract
Tetrahydroisoquinoline-4-carboxylic acid, a constrained β2 -amino acid named β-TIC, was synthesised for the first time in enantiopure form. The biocatalytic route applied herein represents one of the few successful examples of enzymatic resolution of β2 -amino acids. Model tetrapeptides, namely, Fmoc-l-Ala-β-TIC-β-Ala-l-Val-OBn (Fmoc=fluorenylmethyloxycarbonyl, Bn=benzyl), containing both isomers of β-TIC, were prepared. Both computational and NMR spectroscopy studies were performed. A reverse-turn conformation was observed in the case of (R)-β-TIC enantiomer that was obtained in 99 % enantiomeric excess by enzymatic resolution. The β-TIC/β-Ala construct represents the first example of a flexible turn mimetic containing a cyclic and an acyclic β-amino acid. Furthermore, the presence of an aromatic ring of β-TIC could facilitate non-covalent interactions to increase the potential of this scaffold for the preparation of protein-protein interaction modulators.
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Affiliation(s)
- Raffaella Bucci
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Andrea Bonetti
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Francesca Clerici
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Alessandro Contini
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Donatella Nava
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Sara Pellegrino
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
| | - Davide Tessaro
- Department of Chemistry, Materials and, Chemical Engineering "G. Natta", Politecnico di Milano, p.za L. da Vinci 32, 20133, Milano, Italy
| | - Maria Luisa Gelmi
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Università degli Studi Milano, Via Venezian 21, 20133, Milano, Italy
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25
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A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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26
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Ge Y, Kier BL, Andersen NH, Voelz VA. Computational and Experimental Evaluation of Designed β-Cap Hairpins Using Molecular Simulations and Kinetic Network Models. J Chem Inf Model 2017; 57:1609-1620. [PMID: 28614661 DOI: 10.1021/acs.jcim.7b00132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular simulation has been used to model the detailed folding properties of peptides, yet prospective computational peptide design by such approaches remains challenging and nontrivial. To test the accuracy of simulation-based hairpin design, we characterized the folding properties of a series of so-called β-cap hairpin peptides designed to mimic a conserved hairpin of LapD, a bacterial intracellular signaling protein, both experimentally by NMR spectroscopy and computationally by implicit-solvent replica-exchange molecular dynamics using three different AMBER force fields (ff96, ff99sb-ildn, and ff99sb-ildn-NMR). A unique challenge presented by these designs is the presence of both a terminal Trp-Trp capping motif and a conserved GWxQ motif in the hairpin turn required for binding to LapG. Consistent with previous studies, we found AMBER ff96 to be the most accurate when used with the OBC GBSA implicit solvent model, despite its known bias toward β-sheet conformations when used in explicit-solvent simulations. To gain microscopic insight into the folding landscape of the hairpin designs, we additionally performed parallel simulations on the Folding@home distributed computing platform using AMBER ff99sb-ildn-NMR with TIP3P explicit solvent. Markov state models (MSMs) built from trajectory data reveal a number of non-native interactions between Trp and other amino acid side chains, creating potential problems in achieving well-folded hairpin structures in solution.
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Affiliation(s)
- Yunhui Ge
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Brandon L Kier
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Niels H Andersen
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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27
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Smith DJ, Shell MS. Can Simple Interaction Models Explain Sequence-Dependent Effects in Peptide Homodimerization? J Phys Chem B 2017; 121:5928-5943. [PMID: 28537734 DOI: 10.1021/acs.jpcb.7b03186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The development of rapid methods to explain and predict peptide interactions, aggregation, and self-assembly has become important to understanding amyloid disease pathology, the shelf stability of peptide therapeutics, and the design of novel peptide materials. Although experimental aggregation databases have been used to develop correlative and statistical models, molecular simulations offer atomic-level details that potentially provide greater physical insight and allow one to single out the most explanatory simple models. Here, we outline one such approach using a case study that develops homodimerization models for serine-glycine peptides with various hydrophobic leucine mutations. Using detailed all-atom simulations, we calculate reference dimerization free energy profiles and binding constants for a small peptide library. We then use statistical methods to systematically assess whether simple interaction models, which do not require expensive simulations and free energy calculation, can capture them. Surprisingly, some combinations of a few simple scaling laws well recapitulate the detailed, all-atom results with high accuracy. Specifically, we find that a recently proposed phenomenological hydrophobic force law and coarse measures of entropic effects in binding offer particularly high explanatory power, underscoring the physical relevance to association that these driving forces can play.
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Affiliation(s)
- David J Smith
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara , Santa Barbara, California 93106, United States
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28
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Linh NH, Thu TTM, Tu L, Hu CK, Li MS. Impact of Mutations at C-Terminus on Structures and Dynamics of Aβ40 and Aβ42: A Molecular Simulation Study. J Phys Chem B 2017; 121:4341-4354. [DOI: 10.1021/acs.jpcb.6b12888] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nguyen Hoang Linh
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Tran Thi Minh Thu
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - LyAnh Tu
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Biomedical
Engineering Department, University of Technology - VNU HCM
, 268 Ly Thuong
Kiet Street, District 10, Ho Chi Minh City, Vietnam
| | - Chin-Kun Hu
- Institute
of Physics, Academia Sinica
, 128 Academia Road Section 2, Taipei
11529, Taiwan
- National
Center for Theoretical Sciences, National Tsing Hua University
, 101 Kuang-Fu Road Section 2, Hsinch
30013, Taiwan
- Business
School, University of Shanghai for Science and Technology
, 334 Jun
Gong Road, Shanghai
200093, China
| | - Mai Suan Li
- Institute for Computational Science and Technology
, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Institute of Physics Polish Academy of Sciences
, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
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29
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Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. Sci Rep 2017; 7:44116. [PMID: 28272524 PMCID: PMC5341065 DOI: 10.1038/srep44116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/03/2017] [Indexed: 01/25/2023] Open
Abstract
The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.
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30
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Prokopovich DV, Whittaker JW, Muthee MM, Ahmed A, Larini L. Impact of Phosphorylation and Pseudophosphorylation on the Early Stages of Aggregation of the Microtubule-Associated Protein Tau. J Phys Chem B 2017; 121:2095-2103. [PMID: 28218850 DOI: 10.1021/acs.jpcb.7b00194] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The microtubule-associated protein tau regulates the stability of microtubules within neurons in the central nervous system. In turn, microtubules are responsible for the remodeling of the cytoskeleton that ultimately leads to the formation or pruning of new connections among neurons. As a consequence, dysfunction of tau is associated with many forms of dementia as well as Alzheimer's disease. In the brain, tau activity is regulated by its phosphorylation state. Phosphorylation is a post-translational modification of proteins that adds a phosphate group to the side chain of an amino acid. Phosphorylation at key locations in the tau sequence leads to a higher or lower affinity for microtubules. In Alzheimer's disease, tau is present in an abnormal phosphorylation state. However, studying the effect of phosphorylation experimentally has been extremely challenging as there is no viable way of exactly selecting the location and the number of phosphorylated sites. For this reason, researchers have turned to pseudophosphorylation. In this technique, actual phosphorylation is mimicked by mutating the selected amino acid into glutamate or aspartate. Whether this methodology is equivalent to actual phosphorylation is still open to debate. In this study, we will show that phosphorylation and pseudophosphorylation are not exactly equivalent. Although for larger aggregates the two techniques lead to similar structures, the kinetics of the process may be altered. In addition, very little is known about the impact that this may have on the early stages of aggregation, such as nucleation and conformational rearrangement. In this study, we show that the two methods may produce a similar ensemble of conformations, even though the kinetic and chemical details that lead to it are quite different.
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Affiliation(s)
- Dmitriy V Prokopovich
- Department of Physics and ‡Center for Computational and Integrative Biology, Rutgers University-Camden , Camden, New Jersey 08102, United States
| | - John W Whittaker
- Department of Physics and ‡Center for Computational and Integrative Biology, Rutgers University-Camden , Camden, New Jersey 08102, United States
| | - Micaiah M Muthee
- Department of Physics and ‡Center for Computational and Integrative Biology, Rutgers University-Camden , Camden, New Jersey 08102, United States
| | - Azka Ahmed
- Department of Physics and ‡Center for Computational and Integrative Biology, Rutgers University-Camden , Camden, New Jersey 08102, United States
| | - Luca Larini
- Department of Physics and ‡Center for Computational and Integrative Biology, Rutgers University-Camden , Camden, New Jersey 08102, United States
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31
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Tomsett M, Maffucci I, Le Bailly BAF, Byrne L, Bijvoets SM, Lizio MG, Raftery J, Butts CP, Webb SJ, Contini A, Clayden J. A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal. Chem Sci 2017; 8:3007-3018. [PMID: 28451368 PMCID: PMC5380885 DOI: 10.1039/c6sc05474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/24/2017] [Indexed: 11/21/2022] Open
Abstract
Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.
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Affiliation(s)
- Michael Tomsett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Bryden A F Le Bailly
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Stefan M Bijvoets
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - M Giovanna Lizio
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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32
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Robinson MK, Monroe JI, Shell MS. Are AMBER Force Fields and Implicit Solvation Models Additive? A Folding Study with a Balanced Peptide Test Set. J Chem Theory Comput 2016; 12:5631-5642. [DOI: 10.1021/acs.jctc.6b00788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Melina K. Robinson
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jacob I. Monroe
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - M. Scott Shell
- Department
of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
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33
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Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88. J Mol Model 2016; 22:177. [DOI: 10.1007/s00894-016-3027-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
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34
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Thurston BA, Tovar JD, Ferguson AL. Thermodynamics, morphology, and kinetics of early-stage self-assembly of π-conjugated oligopeptides. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1125997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Bryce A. Thurston
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John D. Tovar
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
- Institute of NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew L. Ferguson
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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35
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Ikebe J, Umezawa K, Higo J. Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction. Biophys Rev 2016; 8:45-62. [PMID: 28510144 PMCID: PMC5425738 DOI: 10.1007/s12551-015-0189-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/07/2015] [Indexed: 01/08/2023] Open
Abstract
Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.
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Affiliation(s)
- Jinzen Ikebe
- Molecular Modeling and Simulation Group, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Koji Umezawa
- Department of Pure and Applied Physics, Waseda University, Okubo 3-4-1, Shinjuku-Ku, Tokyo, 169-8555, Japan
| | - Junichi Higo
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
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36
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Maffucci I, Contini A. An Updated Test of AMBER Force Fields and Implicit Solvent Models in Predicting the Secondary Structure of Helical, β-Hairpin, and Intrinsically Disordered Peptides. J Chem Theory Comput 2016; 12:714-27. [DOI: 10.1021/acs.jctc.5b01211] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche
− Sezione di Chimica Generale e Organica “Alessandro
Marchesini”, Università degli Studi di Milano, Via
Venezian, 21 20133 Milano, Italy
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37
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Carmichael SP, Shell MS. Entropic (de)stabilization of surface-bound peptides conjugated with polymers. J Chem Phys 2015; 143:243103. [DOI: 10.1063/1.4929592] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Scott P. Carmichael
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
| | - M. Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, USA
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38
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Han W, Wan CK, Wu YD. PACE Force Field for Protein Simulations. 2. Folding Simulations of Peptides. J Chem Theory Comput 2015; 6:3390-402. [PMID: 26617093 DOI: 10.1021/ct100313a] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We present the application of our recently developed PACE force field to the folding of peptides. These peptides include α-helical (AK17 and Fs), β-sheet (GB1m2 and Trpzip2), and mixed helical/coil (Trp-cage) peptides. With replica exchange molecular dynamics (REMD), our force field can fold the five peptides into their native structures while maintaining their stabilities reasonably well. Our force field is also able to capture important thermodynamic features of the five peptides that have been observed in previous experimental and computational studies, such as different preferences for a helix-turn-helix topology for AK17 and Fs, the relative contribution of four hydrophobic side chains of GB1p to the stability of β-hairpin, and the distinct role of a hydrogen bond involving Trp-Hε and a D9/R16 salt bridge in stabilizing the Trp-cage native structure. Furthermore, multiple folding and unfolding events are observed in our microsecond-long normal MD simulations of AK17, Trpzip2, and Trp-cage. These simulations provide mechanistic information such as a "zip-out" pathway of the folding mechanism of Trpzip2 and the folding times of AK17 and Trp-cage, which are estimated to be about 51 ± 43 ns and 270 ± 110 ns, respectively. A 600 ns simulation of the peptides can be completed within one day. These features of our force field are potentially applicable to the study of thermodynamics and kinetics of real protein systems.
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Affiliation(s)
- Wei Han
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
| | - Cheuk-Kin Wan
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
| | - Yun-Dong Wu
- Department of Chemistry, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong, China, School of Chemical Biology and Biotechnology, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, and College of Chemistry, Peking University, Beijing, China
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39
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Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins 2015; 83:2279-92. [PMID: 26476100 DOI: 10.1002/prot.24947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/11/2015] [Accepted: 09/29/2015] [Indexed: 12/26/2022]
Abstract
The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - M F Thorpe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.,Rudolf Peierls Center for Theoretical Physics, University of Oxford, Oxford, OX1 3NP, United Kingdom
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
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40
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Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations. J Chem Theory Comput 2015; 11:4770-9. [PMID: 26574266 DOI: 10.1021/acs.jctc.5b00662] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbneck2. Ff12SB-cMAP can be downloaded ( https://github.com/laufercenter/Amap.git ) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.
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Affiliation(s)
| | - Justin L MacCallum
- Department of Chemistry, University of Calgary , Calgary, AB T2N 1N4, Canada
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41
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Naz F, Singh P, Islam A, Ahmad F, Imtaiyaz Hassan M. Human microtubule affinity-regulating kinase 4 is stable at extremes of pH. J Biomol Struct Dyn 2015. [PMID: 26208600 DOI: 10.1080/07391102.2015.1074942] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MAP/microtubule affinity-regulating kinase 4 (MARK4) is a member of adenosine monophosphate-activated protein kinases, directly associated with cancer and neurodegenerative diseases. Here, we have cloned, expressed, and purified two variants of MARK4 [the kinase domain (MARK4-F2), and kinase domain along with 59 N-terminal residues (MARK4-F1)] and compared their stability at varying pH range. Structural and functional changes were observed by incubating both forms of MARK4 in buffers of different pH. We measured the secondary structure of MARK4 using circular dichroism and tertiary structure by measuring intrinsic fluorescence and absorbance properties along with the size of proteins by dynamic light scattering. We observed that at extremes of pH (below pH 3.5 and above pH 9.0), MARK4 is quite stable. However, a remarkable aggregate formation was observed at intermediate pH (between pH 3.5 and 9.0). To further validate this result, we have modeled both forms of MARK4 and performed molecular dynamics simulation for 15 ns. The spectroscopic observations are in excellent agreement with the findings of molecular dynamics simulation. We also performed ATPase activity at varying pH and found a significant correlation of structure of MARK4 with its enzyme activity. It is interesting to note that both forms of MARK4 are showing a similar pattern of structure changes with reference to pH.
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Affiliation(s)
- Farha Naz
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Parvesh Singh
- b School of Chemistry and Physics , University of Kwa-Zulu Natal , Chiltern Hill, Durban 4000 , South Africa
| | - Asimul Islam
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Faizan Ahmad
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
| | - Md Imtaiyaz Hassan
- a Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , Jamia Nagar, New Delhi 110025 , India
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42
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Nguyen H, Pérez A, Bermeo S, Simmerling C. Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins. J Chem Theory Comput 2015; 11:3714-28. [PMID: 26574454 PMCID: PMC4805114 DOI: 10.1021/acs.jctc.5b00271] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson-Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software.
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Affiliation(s)
- Hai Nguyen
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Alberto Pérez
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Sherry Bermeo
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
| | - Carlos Simmerling
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology, and §Department of Biochemistry, Stony Brook University , Stony Brook, New York 11794, USA
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43
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Zerze GH, Uz B, Mittal J. Folding thermodynamics ofβ-hairpins studied by replica-exchange molecular dynamics simulations. Proteins 2015; 83:1307-15. [DOI: 10.1002/prot.24827] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Gül H. Zerze
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Bilge Uz
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering; Lehigh University; Bethlehem Pennsylvania 18015
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44
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Ben-Shimon A, Niv MY. AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking. Structure 2015; 23:929-940. [PMID: 25914054 DOI: 10.1016/j.str.2015.03.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 03/20/2015] [Accepted: 03/22/2015] [Indexed: 12/18/2022]
Abstract
The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements.
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Affiliation(s)
- Avraham Ben-Shimon
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Rehovot 76100, Israel
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment and The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Rehovot 76100, Israel.
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45
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Wakefield AE, Wuest WM, Voelz VA. Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides. J Chem Inf Model 2015; 55:806-13. [PMID: 25741627 DOI: 10.1021/ci500768u] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To test the ability of molecular simulations to accurately predict the solution-state conformational properties of peptidomimetics, we examined a test set of 18 cyclic RGD peptides selected from the literature, including the anticancer drug candidate cilengitide, whose favorable binding affinity to integrin has been ascribed to its pre-organization in solution. For each design, we performed all-atom replica-exchange molecular dynamics simulations over several microseconds and compared the results to extensive published NMR data. We find excellent agreement with experimental NOE distance restraints, suggesting that molecular simulation can be a useful tool for the computational design of pre-organized solution-state structure. Moreover, our analysis of conformational populations estimates that, despite the potential for increased flexibility due to backbone amide isomerizaton, N-methylation provides about 0.5 kcal/mol of reduced conformational entropy to cyclic RGD peptides. The combination of pre-organization and binding-site compatibility explains the strong binding affinity of cilengitide to integrin.
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Affiliation(s)
- Amanda E Wakefield
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - William M Wuest
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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46
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Maffucci I, Pellegrino S, Clayden J, Contini A. Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids. J Phys Chem B 2015; 119:1350-61. [PMID: 25528885 DOI: 10.1021/jp510775e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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47
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Hughes ZE, Walsh TR. What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces. J Mater Chem B 2015; 3:3211-3221. [DOI: 10.1039/c5tb00004a] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular dynamics simulations of the aqueous biomolecule–graphene interface have predicted the free energy of adsorption of amino acids and the structure of peptides.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials
- Deakin University
- Geelong
- Australia
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48
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Brown AH, Rodger PM, Evans JS, Walsh TR. Equilibrium Conformational Ensemble of the Intrinsically Disordered Peptide n16N: Linking Subdomain Structures and Function in Nacre. Biomacromolecules 2014; 15:4467-79. [DOI: 10.1021/bm501263s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Aaron H. Brown
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
| | | | - John Spencer Evans
- Department
of Craniofacial Biology and Center for Skeletal Sciences, New York University, New York, New York 10010, United States
| | - Tiffany R. Walsh
- Institute
for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia
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49
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Nguyen H, Maier J, Huang H, Perrone V, Simmerling C. Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and implicit solvent. J Am Chem Soc 2014; 136:13959-62. [PMID: 25255057 PMCID: PMC4195377 DOI: 10.1021/ja5032776] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The millisecond time scale needed for molecular dynamics simulations to approach the quantitative study of protein folding is not yet routine. One approach to extend the simulation time scale is to perform long simulations on specialized and expensive supercomputers such as Anton. Ideally, however, folding simulations would be more economical while retaining reasonable accuracy, and provide feedback on structure, stability and function rapidly enough if partnered directly with experiment. Approaches to this problem typically involve varied compromises between accuracy, precision, and cost; the goal here is to address whether simple implicit solvent models have become sufficiently accurate for their weaknesses to be offset by their ability to rapidly provide much more precise conformational data as compared to explicit solvent. We demonstrate that our recently developed physics-based model performs well on this challenge, enabling accurate all-atom simulated folding for 16 of 17 proteins with a variety of sizes, secondary structure, and topologies. The simulations were carried out using the Amber software on inexpensive GPUs, providing ∼1 μs/day per GPU, and >2.5 ms data presented here. We also show that native conformations are preferred over misfolded structures for 14 of the 17 proteins. For the other 3, misfolded structures are thermodynamically preferred, suggesting opportunities for further improvement.
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Affiliation(s)
- Hai Nguyen
- Department of Chemistry, ‡Laufer Center for Physical and Quantitative Biology and §Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York 11794-5252, United States
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Susa AC, Wu C, Bernstein SL, Dupuis NF, Wang H, Raleigh DP, Shea JE, Bowers MT. Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions. J Am Chem Soc 2014; 136:12912-9. [PMID: 25144879 PMCID: PMC4183647 DOI: 10.1021/ja504031d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Indexed: 11/28/2022]
Abstract
Human islet amyloid polypeptide (hIAPP or Amylin) is a 37 residue hormone that is cosecreted with insulin from the pancreatic islets. The aggregation of hIAPP plays a role in the progression of type 2 diabetes and contributes to the failure of islet cell grafts. Despite considerable effort, little is known about the mode of action of IAPP amyloid inhibitors, and this has limited rational drug design. Insulin is one of the most potent inhibitors of hIAPP fibril formation, but its inhibition mechanism is not understood. In this study, the aggregation of mixtures of hIAPP with insulin, as well as with the separate A and B chains of insulin, were characterized using ion mobility spectrometry-based mass spectrometry and atomic force microscopy. Insulin and the insulin B chain target the hIAPP monomer in its compact isoform and shift the equilibrium away from its extended isoform, an aggregation-prone conformation, and thus inhibit hIAPP from forming β-sheets and subsequently amyloid fibrils. All-atom molecular modeling supports these conclusions.
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Affiliation(s)
- Anna C. Susa
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Chun Wu
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Summer L. Bernstein
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Nicholas F. Dupuis
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Hui Wang
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Joan-Emma Shea
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University
of California, Santa Barbara, California 93106, United States
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