51
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Ostrowska N, Feig M, Trylska J. Modeling Crowded Environment in Molecular Simulations. Front Mol Biosci 2019; 6:86. [PMID: 31572730 PMCID: PMC6749006 DOI: 10.3389/fmolb.2019.00086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/27/2019] [Indexed: 01/09/2023] Open
Abstract
Biomolecules perform their various functions in living cells, namely in an environment that is crowded by many macromolecules. Thus, simulating the dynamics and interactions of biomolecules should take into account not only water and ions but also other binding partners, metabolites, lipids and macromolecules found in cells. In the last decade, research on how to model macromolecular crowders around proteins in order to simulate their dynamics in models of cellular environments has gained a lot of attention. In this mini-review we focus on the models of crowding agents that have been used in computer modeling studies of proteins and peptides, especially via molecular dynamics simulations.
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Affiliation(s)
- Natalia Ostrowska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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52
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Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications. Int J Mol Sci 2019; 20:ijms20153774. [PMID: 31375023 PMCID: PMC6696403 DOI: 10.3390/ijms20153774] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.
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53
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Li ZL, Buck M. Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom Molecular Dynamics Simulations, Confirming a Stepwise Association Process for Native Protein-Protein Interactions. J Chem Theory Comput 2019; 15:4318-4331. [PMID: 31241940 DOI: 10.1021/acs.jctc.9b00195] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The relative prevalence of native protein-protein interactions (PPIs) are the cornerstone for understanding the structure, dynamics and mechanisms of function of protein complexes. In this study, we develop a scheme for scaling the protein-water interaction in the CHARMM36 force field, in order to better fit the solvation free energy of amino acids side-chain analogues. We find that the molecular dynamics simulation with the scaled force field, CHARMM36s, as well as a recently released version, CHARMM36m, effectively improve on the overly sticky association of proteins, such as ubiquitin. We investigate the formation of a heterodimer protein complex between the SAM domains of the EphA2 receptor and the SHIP2 enzyme by performing a combined total of 48 μs simulations with the different potential functions. While the native SAM heterodimer is only predicted at a low rate of 6.7% with the original CHARMM36 force field, the yield is increased to 16.7% with CHARMM36s, and to 18.3% with CHARMM36m. By analyzing the 25 native SAM complexes formed in the simulations, we find that their formation involves a preorientation guided by Coulomb interactions, consistent with an electrostatic steering mechanism. In 12 cases, the complex could directly transform to the native protein interaction surfaces with only small adjustments in domain orientation. In the other 13 cases, orientational and/or translational adjustments are needed to reach the native complex. Although the tendency for non-native complexes to dissociate has nearly doubled with the modified potential functions, a dissociation followed by a reassociation to the correct complex structure is still rare. Instead, the remaining non-native complexes undergo configurational changes/surface searching, which, however, rarely leads to native structures on a time scale of 250 ns. These observations provide a rich picture of the mechanisms of protein-protein complex formation and suggest that computational predictions of native complex PPIs could be improved further.
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Affiliation(s)
- Zhen-Lu Li
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Matthias Buck
- Department of Physiology and Biophysics , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States.,Departments of Pharmacology and Neurosciences, and Case Comprehensive Cancer Center , Case Western Reserve University, School of Medicine , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
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54
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Honegger P, Steinhauser O. Hydration dynamics of proteins in reverse micelles probed by 1H-NOESY/ 1H-ROESY NMR and 17O-nuclear quadrupole resonance (NQR). Phys Chem Chem Phys 2019; 21:14571-14582. [PMID: 31237595 DOI: 10.1039/c9cp02654a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study is based on extensive MD simulations of a protein in a reverse micelle to mimic the effect of confinement on biomolecules. This permits the calculation of measurable quantities appearing in NQR and Nuclear Overhauser-NMR despite the high computational effort. We address the long-standing debate about the intermolecular NOE showing that absolute quantities derived from NOESY and ROESY spectra do indeed contain considerable long-range contributions, while ratios thereof are effectively short-ranged due to almost perfect compensation effects. Based on NQR relaxation times, we predict strong rotational retardation of interstitial water between the protein and the surfactant surface. The computed NOE to ROE ratio correlates fairly with experimental results. The solvation dynamics mapped onto the protein surface reflects the spatial heterogeneity of a cell-like system with slow water dynamics in proximity to the cell wall and almost bulk-like behaviour in the water core.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
| | - Othmar Steinhauser
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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55
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 264] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Indexed: 02/07/2023]
Abstract
Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Besian I. Sejdiu
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haydee Mesa-Galloso
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Haleh Abdizadeh
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute and Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
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56
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Célerse F, Lagardère L, Derat E, Piquemal JP. Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems. J Chem Theory Comput 2019; 15:3694-3709. [DOI: 10.1021/acs.jctc.9b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Frédéric Célerse
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Louis Lagardère
- Institut des Sciences du Calcul et des Données, Sorbonne Université, 75005 Paris, France
- Institut Parisien de Chimie Physique et Théorique, FR 2622 CNRS, Sorbonne Université, 75005 Paris, France
- Laboratoire de Chimie théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Etienne Derat
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
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57
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Zerze GH, Zheng W, Best RB, Mittal J. Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties. J Phys Chem Lett 2019; 10:2227-2234. [PMID: 30990694 PMCID: PMC7507668 DOI: 10.1021/acs.jpclett.9b00850] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Experimental studies on intrinsically disordered and unfolded proteins have shown that in isolation they typically have low populations of secondary structure and exhibit distance scalings suggesting that they are at near-theta-solvent conditions. Until recently, however, all-atom force fields failed to reproduce these fundamental properties of intrinsically disordered proteins (IDPs). Recent improvements by refining against ensemble-averaged experimental observables for polypeptides in aqueous solution have addressed deficiencies including secondary structure bias, global conformational properties, and thermodynamic parameters of biophysical reactions such as folding and collapse. To date, studies utilizing these improved all-atom force fields have mostly been limited to a small set of unfolded or disordered proteins. Here, we present data generated for a diverse library of unfolded or disordered proteins using three progressively improved generations of Amber03 force fields, and we explore how global and local properties are affected by each successive change in the force field. We find that the most recent force field refinements significantly improve the agreement of the global properties such as radii of gyration and end-to-end distances with experimental estimates. However, these global properties are largely independent of the local secondary structure propensity. This result stresses the need to validate force fields with reference to a combination of experimental data providing information about both local and global structure formation.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts , Arizona State University , Mesa , Arizona 85212 , United States
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States
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58
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Sengupta U, Carballo-Pacheco M, Strodel B. Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly. J Chem Phys 2019; 150:115101. [DOI: 10.1063/1.5083915] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Ushnish Sengupta
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Department of Engineering, University of Cambridge, Cambridge CB2 1PZ, United Kingdom
| | - Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- AICES Graduate School, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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59
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Abstract
All-atom, classical force fields for protein molecular dynamics (MD) simulations currently occupy a sweet spot in the universe of computational models, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some biologically relevant time scales (microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad of force field branches in current use, which can make it hard for those entering the simulation field to know which would be the best set of parameters for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.
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Affiliation(s)
- Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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60
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Honegger P, Steinhauser O. Towards capturing cellular complexity: combining encapsulation and macromolecular crowding in a reverse micelle. Phys Chem Chem Phys 2019; 21:8108-8120. [DOI: 10.1039/c9cp00053d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper studies the orientational structure and dynamics of multi-protein systems under confinement and discusses the implications on biological cells.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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61
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Honegger P, Heid E, Schmode S, Schröder C, Steinhauser O. Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect. RSC Adv 2019; 9:36982-36993. [PMID: 35539058 PMCID: PMC9075347 DOI: 10.1039/c9ra08008b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022] Open
Abstract
The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution. Changes in local protein hydration dynamics caused by encapsulation or crowding are reflected in the TDSS and the intermolecular NOE alike.![]()
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Esther Heid
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Stella Schmode
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Christian Schröder
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- Austria
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62
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Abstract
The long lag times and subsequent rapid growth of Alzheimer's Aβ42 fibrils can be explained by a secondary nucleation step, in which existing fibril surfaces are able to nucleate the formation of new fibrils via an autocatalytic process. The molecular mechanism of secondary nucleation, however, is still unknown. Here we investigate the first step, namely, adsorption of the Aβ42 peptide monomers onto the fibril surface. Using long all-atom molecular simulations and an enhanced sampling scheme, we are able to generate a diverse ensemble of binding events. The resulting thermodynamics of adsorption are consistent with experiment as well as with the requirements for effective autocatalysis determined from coarse-grained simulations. We identify the key interactions stabilizing the adsorbed state, which are predominantly polar in nature, and relate them to the effects of known disease-causing mutations.
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Affiliation(s)
- Mathias M J Bellaiche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
- Department of Chemistry , University of Cambridge , Lensfield Road, Cambridge CB2 1EW , United Kingdom
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892-0520 , United States
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63
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Carballo-Pacheco M, Ismail AE, Strodel B. On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6063-6075. [PMID: 30336669 DOI: 10.1021/acs.jctc.8b00579] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22(F19V,F20V), which does not form fibrils, and Aβ16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Ahmed E Ismail
- AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany.,Aachener Verfahrenstechnik, Faculty of Mechanical Engineering , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , 40225 Düsseldorf , Germany
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64
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Ke S, Ulmschneider MB, Wallace BA, Ulmschneider JP. Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel. Biophys J 2018; 115:1920-1930. [PMID: 30366630 DOI: 10.1016/j.bpj.2018.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/09/2023] Open
Abstract
Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the presence of a novel motif consisting of an extensive network of salt bridges involving residues in the voltage sensor, S4-S5 linker, pore, and C-terminal domains. This motif has been proposed to be responsible for maintaining an open conformation that enables ion translocation through the channel. In this study, we have used long-time molecular dynamics calculations without artificial restraints to demonstrate that the interaction network of full-length NavMs indeed prevents a rapid collapse and closure of the gate, in marked difference to earlier studies of the pore-only construct in which the gate had to be restrained to remain open. Interestingly, a frequently discussed "hydrophobic gating" mechanism at nanoscopic level is also observed in our simulations, in which the discontinuous water wire close to the gate region leads to an energetic barrier for ion conduction. In addition, we demonstrate the effects of in silico mutations of several of the key residues in the motif on the open channel's stability and functioning, correlating them with existing functional studies on this channel and homologous disease-associated mutations in human sodium channels; we also examine the effects of truncating/removing the voltage sensor and C-terminal domains in maintaining an open gate.
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Affiliation(s)
- Song Ke
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
| | | | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
| | - Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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65
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Bashardanesh Z, van der Spoel D. Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids. J Phys Chem B 2018; 122:8018-8027. [DOI: 10.1021/acs.jpcb.8b05770] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zahedeh Bashardanesh
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, P.O. Box 596, SE-75124 Uppsala, Sweden
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66
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Zhang H, Jiang Y, Cui Z, Yin C. Force Field Benchmark of Amino Acids. 2. Partition Coefficients between Water and Organic Solvents. J Chem Inf Model 2018; 58:1669-1681. [DOI: 10.1021/acs.jcim.8b00493] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Yang Jiang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Ziheng Cui
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, 100029 Beijing, China
| | - Chunhua Yin
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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67
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Fogolari F, Maloku O, Dongmo Foumthuim CJ, Corazza A, Esposito G. PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles. J Chem Inf Model 2018; 58:1319-1324. [DOI: 10.1021/acs.jcim.8b00143] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Federico Fogolari
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DIMF), University of Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d’Oro 305, 00136 Roma, Italy
| | - Ornela Maloku
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DIMF), University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | | | - Alessandra Corazza
- Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d’Oro 305, 00136 Roma, Italy
- Dipartimento di Area Medica (DAME), University of Udine, Piazzale Kolbe 4, 33100 Udine, Italy
| | - Gennaro Esposito
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche (DIMF), University of Udine, Via delle Scienze 206, 33100 Udine, Italy
- Istituto Nazionale Biostrutture e Biosistemi, Viale medaglie d’Oro 305, 00136 Roma, Italy
- Science and Math Division, New York University at Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
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68
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Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7480749. [PMID: 29967786 PMCID: PMC6008865 DOI: 10.1155/2018/7480749] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/06/2018] [Indexed: 12/15/2022]
Abstract
Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR), i.e., the double mutant F87M/L110M (MT-TTR) and the triple mutant F87M/L110M/S117E (3M-TTR), in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets) appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
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69
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Setiawan D, Brender J, Zhang Y. Recent advances in automated protein design and its future challenges. Expert Opin Drug Discov 2018; 13:587-604. [PMID: 29695210 DOI: 10.1080/17460441.2018.1465922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Protein function is determined by protein structure which is in turn determined by the corresponding protein sequence. If the rules that cause a protein to adopt a particular structure are understood, it should be possible to refine or even redefine the function of a protein by working backwards from the desired structure to the sequence. Automated protein design attempts to calculate the effects of mutations computationally with the goal of more radical or complex transformations than are accessible by experimental techniques. Areas covered: The authors give a brief overview of the recent methodological advances in computer-aided protein design, showing how methodological choices affect final design and how automated protein design can be used to address problems considered beyond traditional protein engineering, including the creation of novel protein scaffolds for drug development. Also, the authors address specifically the future challenges in the development of automated protein design. Expert opinion: Automated protein design holds potential as a protein engineering technique, particularly in cases where screening by combinatorial mutagenesis is problematic. Considering solubility and immunogenicity issues, automated protein design is initially more likely to make an impact as a research tool for exploring basic biology in drug discovery than in the design of protein biologics.
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Affiliation(s)
- Dani Setiawan
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - Jeffrey Brender
- b Radiation Biology Branch , Center for Cancer Research, National Cancer Institute - NIH , Bethesda , MD , USA
| | - Yang Zhang
- a Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor , MI , USA.,c Department of Biological Chemistry , University of Michigan , Ann Arbor , MI , USA
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70
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Zhang H, Yin C, Jiang Y, van der Spoel D. Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. J Chem Inf Model 2018; 58:1037-1052. [DOI: 10.1021/acs.jcim.8b00026] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Chunhua Yin
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Jiang
- Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Box 53, Beijing 100029, China
| | - David van der Spoel
- Uppsala Center for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-75124 Uppsala, Sweden
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71
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Yoo J, Aksimentiev A. New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions. Phys Chem Chem Phys 2018; 20:8432-8449. [PMID: 29547221 DOI: 10.1039/c7cp08185e] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to an assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity. However, advances in parallel computing technology have outpaced the development of the underlying theoretical models-the molecular force fields, pushing the MD method into an untested territory. Recent tests of the MD method have found the most commonly used molecular force fields to be out of balance, overestimating attractive interactions between charged and hydrophobic groups, which can promote artificial aggregation in MD simulations of multi-component protein, nucleic acid, and lipid systems. One route towards improving the force fields is through the NBFIX corrections method, in which the intermolecular forces are calibrated against experimentally measured quantities such as osmotic pressure by making atom pair-specific adjustments to the non-bonded interactions. In this article, we review development of the NBFIX (Non-Bonded FIX) corrections to the AMBER and CHARMM force fields and discuss their implications for MD simulations of electrolyte solutions, dense DNA systems, Holliday junctions, protein folding, and lipid bilayer membranes.
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Affiliation(s)
- Jejoong Yoo
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA. and Center for Self-assembly and Complexity, Institute for Basic Science, Pohang, 37363, Republic of Korea
| | - Aleksei Aksimentiev
- Center for the Physics of Living Cells, Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
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72
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Paul F, Noé F, Weikl TR. Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J Phys Chem B 2018. [PMID: 29522679 DOI: 10.1021/acs.jpcb.7b12146] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unstructured proteins and peptides typically fold during binding to ligand proteins. A challenging problem is to identify the mechanism and kinetics of these binding-induced folding processes in experiments and atomistic simulations. In this Article, we present a detailed picture for the folding of the inhibitor peptide PMI into a helix during binding to the oncoprotein fragment 25-109Mdm2 obtained from atomistic, explicit-water simulations and Markov state modeling. We find that binding-induced folding of PMI is highly parallel and can occur along a multitude of pathways. Some pathways are induced-fit-like with binding occurring prior to PMI helix formation, while other pathways are conformational-selection-like with binding after helix formation. On the majority of pathways, however, binding is intricately coupled to folding, without clear temporal ordering. A central feature of these pathways is PMI motion on the Mdm2 surface, along the binding groove of Mdm2 or over the rim of this groove. The native binding groove of Mdm2 thus appears as an asymmetric funnel for PMI binding. Overall, binding-induced folding of PMI does not fit into the classical picture of induced fit or conformational selection that implies a clear temporal ordering of binding and folding events. We argue that this holds in general for binding-induced folding processes because binding and folding events in these processes likely occur on similar time scales and do exhibit the time-scale separation required for temporal ordering.
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Affiliation(s)
- Fabian Paul
- Max Planck Institute of Colloids and Interfaces , Department of Theory and Bio-Systems , Science Park Golm , 14424 Potsdam , Germany.,Freie Universität Berlin , Department of Mathematics and Computer Science , Arnimallee 6 , 14195 Berlin , Germany
| | - Frank Noé
- Freie Universität Berlin , Department of Mathematics and Computer Science , Arnimallee 6 , 14195 Berlin , Germany
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces , Department of Theory and Bio-Systems , Science Park Golm , 14424 Potsdam , Germany
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73
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Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments. COMPUTATION 2018. [DOI: 10.3390/computation6010015] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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74
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Honegger P, Steinhauser O. Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation. Phys Chem Chem Phys 2018; 20:22932-22945. [DOI: 10.1039/c8cp03422b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mechanism of depolarization in reverse micelles with zwitterionic surfactants and containing polar species but lacking ions is reported.
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Affiliation(s)
- Philipp Honegger
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
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75
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Honegger P, Schmollngruber M, Steinhauser O. Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions. Phys Chem Chem Phys 2018; 20:19581-19594. [DOI: 10.1039/c8cp02360c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive computational studies of ubiquitin crowding with a special focus on protein hydration directly visible in dielectric spectra.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Michael Schmollngruber
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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76
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Banerjee P, Wehle M, Lipowsky R, Santer M. A molecular dynamics model for glycosylphosphatidyl-inositol anchors: “flop down” or “lollipop”? Phys Chem Chem Phys 2018; 20:29314-29324. [DOI: 10.1039/c8cp04059a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational model for GPI anchors tested in DMPC and POPC bilayers. The free anchor rarely occurs as an erected “lollipop-like” conformation, it rather “flops down” onto the bilayer surface. Yet an attached protein (here green fluorescent protein) exhibits extensive orientational flexibility due to the phospho-ethanolamine linker.
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Affiliation(s)
- Pallavi Banerjee
- Department of Theory and Biosystems
- Max Planck Institute for Colloids and Interfaces
- 14424 Potsdam
- Germany
| | - Marko Wehle
- Department of Theory and Biosystems
- Max Planck Institute for Colloids and Interfaces
- 14424 Potsdam
- Germany
| | - Reinhard Lipowsky
- Department of Theory and Biosystems
- Max Planck Institute for Colloids and Interfaces
- 14424 Potsdam
- Germany
| | - Mark Santer
- Department of Theory and Biosystems
- Max Planck Institute for Colloids and Interfaces
- 14424 Potsdam
- Germany
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77
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Watts CR, Gregory A, Frisbie C, Lovas S. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins 2017; 86:279-300. [PMID: 29235155 DOI: 10.1002/prot.25439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/10/2017] [Indexed: 12/14/2022]
Abstract
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.
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Affiliation(s)
- Charles R Watts
- Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota.,Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Andrew Gregory
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Cole Frisbie
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin.,Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
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78
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Nawrocki G, Wang PH, Yu I, Sugita Y, Feig M. Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation. J Phys Chem B 2017; 121:11072-11084. [PMID: 29151345 PMCID: PMC5951686 DOI: 10.1021/acs.jpcb.7b08785] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For a long time, the effect of a crowded cellular environment on protein dynamics has been largely ignored. Recent experiments indicate that proteins diffuse more slowly in a living cell than in a diluted solution, and further studies suggest that the diffusion depends on the local surroundings. Here, detailed insight into how diffusion depends on protein-protein contacts is presented based on extensive all-atom molecular dynamics simulations of concentrated villin headpiece solutions. After force field adjustments in the form of increased protein-water interactions to reproduce experimental data, translational and rotational diffusion was analyzed in detail. Although internal protein dynamics remained largely unaltered, rotational diffusion was found to slow down more significantly than translational diffusion as the protein concentration increased. The decrease in diffusion is interpreted in terms of a transient formation of protein clusters. These clusters persist on sub-microsecond time scales and follow distributions that increasingly shift toward larger cluster size with increasing protein concentrations. Weighting diffusion coefficients estimated for different clusters extracted from the simulations with the distribution of clusters largely reproduces the overall observed diffusion rates, suggesting that transient cluster formation is a primary cause for a slow-down in diffusion upon crowding with other proteins.
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Affiliation(s)
- Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
| | - Po-hung Wang
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Isseki Yu
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN iTHES, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States
- RIKEN Quantitative Biology Center, Integrated Innovation Building 7F, 6-7-1 Minaotojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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79
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Bakarić D, Petrov D, Mouvenchery YK, Heiβler S, Oostenbrink C, Schaumann GE. Ion-induced modification of the sucrose network and its impact on melting of freeze-dried liposomes. DSC and molecular dynamics study. Chem Phys Lipids 2017; 210:38-46. [PMID: 29179944 DOI: 10.1016/j.chemphyslip.2017.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 11/14/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023]
Abstract
Disaccharides play an important role in survival of anhydrobiotic organisms during extreme environmental conditions. A key protection feature is their capability to form the hydrogen bond (HB) network in a similar fashion as the one made by water. Since various ions also affect the HB network in completely hydrated systems, it is of a great interest to understand how they impact preservation when incorporated in a disaccharide network. To address this, we employ a combination of experimental and modeling techniques to study behavior of multilamellar 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes freeze-dried with sucrose in presence of NaCl or NaH2PO4·H2O at various concentrations (0.01-1M). Differential scanning calorimetry (DSC) was employed in order to determine the cooperative unit size (CUS), the number of lipid molecules that constitute a domain of cooperative motion in the liposome, and the melting temperature (Tm). In the absence of salt CUS was estimated to be 122±12, whereas in the presence of NaCl CUS increases more (347±34 for c=1M) than for NaH2PO4·H2O (193±26 for 1M). When it comes to Tm, the situation is reversed; NaCl induces increase by about 1K, while NaH2PO4·H2O by about 10K. These findings clearly demonstrate how different interaction forces-hydrogen bonding, charge pairing, and van der Waals interactions between acyl chains-affect CUS and Tm. Their interplay and contribution of particular interaction was further analyzed with molecular dynamics (MD) simulations. This analysis demonstrated that the HB network of DMPC and sucrose is partially disrupted in the presence of NaCl ions, and even to a greater extent in the case of NaH2PO4·H2O ions. Notably, H2PO4- ions outcompete and replace the sucrose molecules at the DMPC surface, which in turn alters the nature of the DMPC-surrounding interactions, from a weaker HB-dominated to a stronger CP-dominated interaction network.
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Affiliation(s)
- Danijela Bakarić
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany.
| | - Dražen Petrov
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Yamuna Kunhi Mouvenchery
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany
| | - Stefan Heiβler
- Institute for Functional Interfaces, Karlsruhe Institute for Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Chris Oostenbrink
- Department of Material Sciences and Process Engineering, Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Gabriele E Schaumann
- University of Koblenz-Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, Fortstraße 7, D-76829 Landau, Germany.
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80
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Hu D, Zhao W, Zhu Y, Ai H, Kang B. Bead‐Level Characterization of Early‐Stage Amyloid β
42
Aggregates: Nuclei and Ionic Concentration Effects. Chemistry 2017; 23:16257-16273. [PMID: 28792099 DOI: 10.1002/chem.201702388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Dingkun Hu
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials School of Chemistry and Chemical Engineering University of Jinan No. 336, West Road of Nan Xinzhuang Jinan Shandong 250022 P. R. China
| | - Wei Zhao
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials School of Chemistry and Chemical Engineering University of Jinan No. 336, West Road of Nan Xinzhuang Jinan Shandong 250022 P. R. China
| | - Yong Zhu
- Hospital in University of Jinan University of Jinan No. 336, West Road of Nan Xinzhuang Jinan Shandong 250022 P. R. China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials School of Chemistry and Chemical Engineering University of Jinan No. 336, West Road of Nan Xinzhuang Jinan Shandong 250022 P. R. China
| | - Baotao Kang
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials School of Chemistry and Chemical Engineering University of Jinan No. 336, West Road of Nan Xinzhuang Jinan Shandong 250022 P. R. China
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81
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Shamsi Z, Moffett AS, Shukla D. Enhanced unbiased sampling of protein dynamics using evolutionary coupling information. Sci Rep 2017; 7:12700. [PMID: 28983093 PMCID: PMC5629199 DOI: 10.1038/s41598-017-12874-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 09/14/2017] [Indexed: 12/25/2022] Open
Abstract
One of the major challenges in atomistic simulations of proteins is efficient sampling of pathways associated with rare conformational transitions. Recent developments in statistical methods for computation of direct evolutionary couplings between amino acids within and across polypeptide chains have allowed for inference of native residue contacts, informing accurate prediction of protein folds and multimeric structures. In this study, we assess the use of distances between evolutionarily coupled residues as natural choices for reaction coordinates which can be incorporated into Markov state model-based adaptive sampling schemes and potentially used to predict not only functional conformations but also pathways of conformational change, protein folding, and protein-protein association. We demonstrate the utility of evolutionary couplings in sampling and predicting activation pathways of the β 2-adrenergic receptor (β 2-AR), folding of the FiP35 WW domain, and dimerization of the E. coli molybdopterin synthase subunits. We find that the time required for β 2-AR activation and folding of the WW domain are greatly diminished using evolutionary couplings-guided adaptive sampling. Additionally, we were able to identify putative molybdopterin synthase association pathways and near-crystal structure complexes from protein-protein association simulations.
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Affiliation(s)
- Zahra Shamsi
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, 61801, USA
| | - Alexander S Moffett
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, 61801, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL, 61801, USA.
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA.
- National Center for Supercomputing Applications, University of Illinois, Urbana, IL, 61801, USA.
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82
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Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg CP, Sikora M. Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides. J Chem Theory Comput 2017; 13:5039-5053. [DOI: 10.1021/acs.jctc.7b00374] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Felix Deluweit
- Wyatt Technology Europe, Hochstraße
18, 56307 Dernbach, Germany
| | - Roger Scherrers
- Wyatt Technology Europe, Hochstraße
18, 56307 Dernbach, Germany
| | | | - Mateusz Sikora
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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83
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Mercadante D, Wagner JA, Aramburu IV, Lemke EA, Gräter F. Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins. J Chem Theory Comput 2017; 13:3964-3974. [DOI: 10.1021/acs.jctc.7b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Davide Mercadante
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Johannes A. Wagner
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
| | - Iker V. Aramburu
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frauke Gräter
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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84
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Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
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85
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Mazumder A, Batabyal S, Mondal M, Mondol T, Choudhury S, Ghosh R, Chatterjee T, Bhattacharyya D, Pal SK, Roy S. Specific DNA sequences allosterically enhance protein-protein interaction in a transcription factor through modulation of protein dynamics: implications for specificity of gene regulation. Phys Chem Chem Phys 2017; 19:14781-14792. [PMID: 28548177 DOI: 10.1039/c7cp01193h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Most genes are regulated by multiple transcription factors, often assembling into multi-protein complexes in the gene regulatory region. Understanding of the molecular origin of specificity of gene regulatory complex formation in the context of the whole genome is currently inadequate. A phage transcription factor λ-CI forms repressive multi-protein complexes by binding to multiple binding sites in the genome to regulate the lifecycle of the phage. The protein-protein interaction between two DNA-bound λ-CI molecules is stronger when they are bound to the correct pair of binding sites, suggesting allosteric transmission of recognition of correct DNA sequences to the protein-protein interaction interface. Exploration of conformation and dynamics by time-resolved fluorescence anisotropy decay and molecular dynamics suggests a change in protein dynamics to be a crucial factor in mediating allostery. A lattice-based model suggests that DNA-sequence induced allosteric effects could be crucial underlying factors in differentially stabilizing the correct site-specific gene regulatory complexes. We conclude that transcription factors have evolved multiple mechanisms to augment the specificity of DNA-protein interactions in order to achieve an extraordinarily high degree of spatial and temporal specificities of gene regulatory complexes, and DNA-sequence induced allostery plays an important role in the formation of sequence-specific gene regulatory complexes.
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Affiliation(s)
- Abhishek Mazumder
- Division of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700 032, India
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86
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Miller MS, Lay WK, Li S, Hacker WC, An J, Ren J, Elcock AH. Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations. J Chem Theory Comput 2017; 13:1812-1826. [PMID: 28296391 PMCID: PMC5543770 DOI: 10.1021/acs.jctc.6b01059] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparametrize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models. In general, for both the amino acids and the small molecules, the tested force fields produce computed osmotic coefficients that are lower than experiment; this is indicative of excessively favorable solute-solute interactions. The sole exception to this general trend is provided by GROMOS54a7 when applied to amino acids: in this case, the computed osmotic coefficients are consistently too high. Importantly, we show that all of the force fields tested can be made to accurately reproduce the experimental osmotic coefficients of the amino acids when minor modifications-some previously reported by others and some that are new to this study-are made to the van der Waals interactions of the charged terminal groups. Special care is required, however, when simulating Proline with a number of the force fields, and a hydroxyl-group specific modification is required in order to correct Serine and Threonine when simulated with AMBER ff99SB-ILDN. Interestingly, an alternative parametrization of the van der Waals interactions in the latter force field, proposed by the Nerenberg and Head-Gordon groups, is shown to immediately produce osmotic coefficients that are in excellent agreement with experiment. Overall, this study reinforces the idea that osmotic coefficient measurements can be used to identify general shortcomings in commonly used force fields' descriptions of solute-solute interactions and further demonstrates that modifications to van der Waals parameters provide a simple route to optimizing agreement with experiment.
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Affiliation(s)
- Mark S. Miller
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Wesley K. Lay
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Shuxiang Li
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | | | - Jiadi An
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Jianlan Ren
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
| | - Adrian H. Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242
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87
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Bomblies R, Luitz MP, Scanu S, Madl T, Zacharias M. Transient helicity in intrinsically disordered Axin-1 studied by NMR spectroscopy and molecular dynamics simulations. PLoS One 2017; 12:e0174337. [PMID: 28355271 PMCID: PMC5371316 DOI: 10.1371/journal.pone.0174337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/07/2017] [Indexed: 11/18/2022] Open
Abstract
Many natural proteins are, as a whole or in part, intrinsically disordered. Frequently, such intrinsically disordered regions (IDRs) undergo a transition to a defined and often helical conformation upon binding to partner molecules. The intrinsic propensity of an IDR sequence to fold into a helical conformation already in the absence of a binding partner can have a decisive influence on the binding process and affinity. Using a combination of NMR spectroscopy and molecular dynamics (MD) simulations we have investigated the tendency of regions of Axin-1, an intrinsically disordered scaffolding protein of the WNT signaling pathway, to form helices in segments interacting with binding partners. Secondary chemical shifts from NMR measurements show an increased helical population in these regions. Systematic application of MD advanced sampling approaches on peptide segments of Axin-1 reproduces the experimentally observed tendency and allows insights into the distribution of segment conformations and free energies of helix formation. The results, however, were found to dependent on the force field water model. Recent water models specifically designed for IDRs significantly reduce the predicted helical content and do not improve the agreement with experiment.
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Affiliation(s)
- Rainer Bomblies
- Physik-Department, Technische Universität München, Garching, Germany
| | | | - Sandra Scanu
- Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Institute of Structural Biology Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Molecular Biology & Biochemistry Center of Molecular Medicine, Medical University of Graz, Graz, Austria
| | - Martin Zacharias
- Physik-Department, Technische Universität München, Garching, Germany
- * E-mail:
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88
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Wang PH, Yu I, Feig M, Sugita Y. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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89
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Emperador A, Orozco M. Discrete Molecular Dynamics Approach to the Study of Disordered and Aggregating Proteins. J Chem Theory Comput 2017; 13:1454-1461. [PMID: 28157327 DOI: 10.1021/acs.jctc.6b01153] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a refinement of the Coarse Grained PACSAB force field for Discrete Molecular Dynamics (DMD) simulations of proteins in aqueous conditions. As the original version, the refined method provides good representation of the structure and dynamics of folded proteins but provides much better representations of a variety of unfolded proteins, including some very large, impossible to analyze by atomistic simulation methods. The PACSAB/DMD method also reproduces accurately aggregation properties, providing good pictures of the structural ensembles of proteins showing a folded core and an intrinsically disordered region. The combination of accuracy and speed makes the method presented here a good alternative for the exploration of unstructured protein systems.
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Affiliation(s)
- Agustí Emperador
- Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Parc Científic de Barcelona , Josep Samitier 1-5, Barcelona 08028, Spain.,Joint IRB-BSC Program on Computational Biology , Barcelona 08028, Spain.,Departament de Bioquímica i Biomedicina, Facultat de Biología, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
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90
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Gao Y, Zhang C, Zhang JZH, Mei Y. Evaluation of the Coupled Two-Dimensional Main Chain Torsional Potential in Modeling Intrinsically Disordered Proteins. J Chem Inf Model 2017; 57:267-274. [PMID: 28095698 DOI: 10.1021/acs.jcim.6b00589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Intrinsically disordered proteins (IDPs) carry out crucial biological functions in essential biological processes of life. Because of the highly dynamic and conformationally heterogeneous nature of the disordered states of IDPs, molecular dynamics simulations are becoming an indispensable tool for the investigation of the conformational ensembles and dynamic properties of IDPs. Nevertheless, there is still no consensus on the most reliable force field in molecular dynamics simulations for IDPs hitherto. In this work, the recently proposed AMBER99SB2D force field is evaluated in modeling some disordered polypeptides and proteins by checking its ability to reproduce experimental NMR data. The results highlight that when the ildn side-chain corrections are included, AMBER99SB2D-ildn exhibits reliable results that agree with experiments compared with its predecessors, the AMBER14SB, AMBER99SB, AMBER99SB-ildn, and AMBER99SB2D force fields, and that decreasing the overall magnitude of protein-protein interactions in favor of protein-water interactions is a key ingredient behind the improvement.
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Affiliation(s)
- Ya Gao
- College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China
| | - Chaomin Zhang
- College of Fundamental Studies, Shanghai University of Engineering Science , Shanghai 201620, China
| | - John Z H Zhang
- College of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China
| | - Ye Mei
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University , Taiyuan, Shanxi 030006, China.,State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University , Shanghai 200062, China
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91
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Casanovas J, Zanuy D, Alemán C. Distribution of dopant ions around poly(3,4-ethylenedioxythiophene) chains: a theoretical study. Phys Chem Chem Phys 2017; 19:9889-9899. [DOI: 10.1039/c7cp00857k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of counterions and multiple polymer chains on the properties and structure of poly(3,4-ethylenedioxythiophene) (PEDOT) doped with ClO4− has been examined using density functional theory (DFT) calculations with periodic boundary conditions (PBCs).
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Affiliation(s)
- Jordi Casanovas
- Departament de Química
- Escola Politècnica Superior
- Universitat de Lleida
- Lleida E-25001
- Spain
| | - David Zanuy
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Sant Adriá del Besòs
- Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química
- EEBE
- Universitat Politècnica de Catalunya
- Sant Adriá del Besòs
- Spain
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92
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Levine ZA, Shea JE. Simulations of disordered proteins and systems with conformational heterogeneity. Curr Opin Struct Biol 2016; 43:95-103. [PMID: 27988422 DOI: 10.1016/j.sbi.2016.11.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/07/2016] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) and protein regions can facilitate a wide variety of complex physiological processes such as binding, signaling, and formation of membraneless organelles. They can however also play pathological roles by aggregating into cytotoxic oligomers and fibrils. Characterizing the structure and function of disordered proteins is an onerous task, primarily because these proteins adopt transient structures, which are difficult to capture in experiments. Simulations have emerged as a powerful tool for interpreting and augmenting experimental measurements of IDPs. In this review we focus on computer simulations of disordered protein structures, functions, assemblies, and emerging questions that, taken together, give an overview of the field as it exists today.
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Affiliation(s)
- Zachary A Levine
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA 93106, USA; Department of Physics, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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93
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Yu I, Mori T, Ando T, Harada R, Jung J, Sugita Y, Feig M. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm. eLife 2016; 5. [PMID: 27801646 PMCID: PMC5089862 DOI: 10.7554/elife.19274] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/28/2016] [Indexed: 12/24/2022] Open
Abstract
Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology.
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Affiliation(s)
- Isseki Yu
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan
| | - Takaharu Mori
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan
| | - Tadashi Ando
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan
| | - Ryuhei Harada
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Jaewoon Jung
- Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Yuji Sugita
- iTHES Research Group, RIKEN, Saitama, Japan.,Theoretical Molecular Science Laboratory, RIKEN, Saitama, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan.,Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Kobe, Japan
| | - Michael Feig
- Laboratory for Biomolecular Function Simulation, RIKEN Quantitative Biology Center, Kobe, Japan.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
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94
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Fogarty AC, Potestio R, Kremer K. A multi-resolution model to capture both global fluctuations of an enzyme and molecular recognition in the ligand-binding site. Proteins 2016; 84:1902-1913. [PMID: 27699855 DOI: 10.1002/prot.25173] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/07/2016] [Accepted: 09/16/2016] [Indexed: 11/11/2022]
Abstract
In multi-resolution simulations, different system components are simultaneously modeled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of ligand binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modeled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically. This multi-resolution methodology can successfully model stable ligand binding, and we further confirm its validity by exploring the reproduction of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function. Proteins 2016; 84:1902-1913. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Aoife C Fogarty
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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95
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Temperature-sensitive gating of TRPV1 channel as probed by atomistic simulations of its trans- and juxtamembrane domains. Sci Rep 2016; 6:33112. [PMID: 27612191 PMCID: PMC5017144 DOI: 10.1038/srep33112] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022] Open
Abstract
Heat-activated transient receptor potential channel TRPV1 is one of the most studied eukaryotic proteins involved in temperature sensation. Upon heating, it exhibits rapid reversible pore gating, which depolarizes neurons and generates action potentials. Underlying molecular details of such effects in the pore region of TRPV1 is of a crucial importance to control temperature responses of the organism. Despite the spatial structure of the channel in both open (O) and closed (C) states is known, microscopic nature of channel gating and mechanism of thermal sensitivity are still poorly understood. In this work, we used unrestrained atomistic molecular dynamics simulations of TRPV1 (without N- and C-terminal cytoplasmic domains) embedded into explicit lipid bilayer in its O- and C-states. We found that the pore domain with its neighboring loops undergoes large temperature-dependent conformational transitions in an asymmetric way, when fragments of only one monomer move with large amplitude, freeing the pore upon heating. Such an asymmetrical gating looks rather biologically relevant because it is faster and more reliable than traditionally proposed “iris-like” symmetric scheme of channel opening. Analysis of structural, dynamic, and hydrophobic organization of the pore domain revealed entropy growth upon TRPV1 gating, which is in line with current concepts of thermal sensitivity.
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96
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Henriques J, Skepö M. Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P-D Water Model and the Representativeness of Protein Disorder Models. J Chem Theory Comput 2016; 12:3407-15. [PMID: 27243806 DOI: 10.1021/acs.jctc.6b00429] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [ Henriques et al. J. Chem. Theory Comput. 2015 , 11 , 3420 - 3431 ], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues.
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Affiliation(s)
- João Henriques
- Division of Theoretical Chemistry, Lund University , Post Office Box 124, S-221 00 Lund, Sweden
| | - Marie Skepö
- Division of Theoretical Chemistry, Lund University , Post Office Box 124, S-221 00 Lund, Sweden
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97
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Chua KP, Chew LY, Mu Y. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126. Proteins 2016; 84:1134-46. [DOI: 10.1002/prot.25060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/14/2016] [Accepted: 04/28/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Khi Pin Chua
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
| | - Lock Yue Chew
- Interdisciplinary Graduate School; Nanyang Technological University; 637551 Singapore
- Complexity Institute, Nanyang Technological University; 637551 Singapore
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences; Nanyang Technological University; 637551 Singapore
| | - Yuguang Mu
- School of Biological Sciences; Nanyang Technological University; 637551 Singapore
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98
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Miller MS, Lay WK, Elcock AH. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization. J Phys Chem B 2016; 120:8217-29. [PMID: 27052117 DOI: 10.1021/acs.jpcb.6b01902] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium/carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by rederiving the partial charges for each peptide.
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Affiliation(s)
- Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Wesley K Lay
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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99
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Schön JC, Oligschleger C, Cortes J. Prediction and clarification of structures of (bio)molecules on surfaces. ACTA ACUST UNITED AC 2016. [DOI: 10.1515/znb-2015-0222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.
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Affiliation(s)
- J. Christian Schön
- Max-Planck-Institute for Solid State Research , Heisenbergstr. 1, D-70569 Stuttgart, Germany
| | - Christina Oligschleger
- University of Applied Sciences Bonn-Rhein-Sieg , Von-Liebigstr. 20, D-53359 Rheinbach, Germany
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100
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Carballo-Pacheco M, Strodel B. Advances in the Simulation of Protein Aggregation at the Atomistic Scale. J Phys Chem B 2016; 120:2991-9. [PMID: 26965454 DOI: 10.1021/acs.jpcb.6b00059] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation into highly structured amyloid fibrils is associated with various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. Amyloids can also have normal biological functions and, in the future, could be used as the basis for novel nanoscale materials. However, a full understanding of the physicochemical forces that drive protein aggregation is still lacking. Such understanding is crucial for the development of drugs that can effectively inhibit aberrant amyloid aggregation and for the directed design of functional amyloids. Atomistic simulations can help understand protein aggregation. In particular, atomistic simulations can be used to study the initial formation of toxic oligomers which are hard to characterize experimentally and to understand the difference in aggregation behavior between different amyloidogenic peptides. Here, we review the latest atomistic simulations of protein aggregation, concentrating on amyloidogenic protein fragments, and provide an outlook for the future in this field.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich, 52425 Jülich, Germany.,AICES Graduate School, RWTH Aachen University , Schinkelstraße 2, 52062 Aachen, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry , Forschungszentrum Jülich, 52425 Jülich, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, 40225 Düsseldorf, Germany
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