1
|
Investigation of the conformational space of hydrophobic-polar heteropolymers by gyration tensor based parameters. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
2
|
Wilson MS, Landau DP. Thermodynamics of hydrophobic-polar model proteins on the face-centered cubic lattice. Phys Rev E 2021; 104:025303. [PMID: 34525583 DOI: 10.1103/physreve.104.025303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
The HP model, a coarse-grained protein representation with only hydrophobic (H) and polar (P) amino acids, has already been extensively studied on the simple cubic (SC) lattice. However, this geometry severely restricts possible bond angles, and a simple improvement is to instead use the face-centered cubic (fcc) lattice. In this paper, the density of states and ground state energies are calculated for several benchmark HP sequences on the fcc lattice using the replica-exchange Wang-Landau algorithm and a powerful set of Monte Carlo trial moves. Results from the fcc lattice proteins are directly compared with those obtained from a previous lattice protein folding study with a similar methodology on the SC lattice. A thermodynamic analysis shows comparable folding behavior between the two lattice geometries, but with a greater rate of hydrophobic-core formation persisting into lower temperatures on the fcc lattice.
Collapse
Affiliation(s)
- Matthew S Wilson
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
3
|
Farris ACK, Seaton DT, Landau DP. Effects of lattice constraints in coarse-grained protein models. J Chem Phys 2021; 154:084903. [PMID: 33639740 DOI: 10.1063/5.0038184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods-Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-"neutral"-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature-the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining.
Collapse
Affiliation(s)
- Alfred C K Farris
- Department of Physics and Astronomy, Oxford College of Emory University, Oxford, Georgia 30054, USA
| | - Daniel T Seaton
- Open Learning, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
4
|
Vernizzi G, Nguyen TD, Orland H, Olvera de la Cruz M. Multicanonical Monte Carlo ensemble growth algorithm. Phys Rev E 2020; 101:021301. [PMID: 32168705 DOI: 10.1103/physreve.101.021301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/03/2020] [Indexed: 11/07/2022]
Abstract
We present an ensemble Monte Carlo growth method to sample the equilibrium thermodynamic properties of random chains. The method is based on the multicanonical technique of computing the density of states in the energy space. Such a quantity is temperature independent, and therefore microcanonical and canonical thermodynamic quantities, including the free energy, entropy, and thermal averages, can be obtained by reweighting with a Boltzmann factor. The algorithm we present combines two approaches: The first is the Monte Carlo ensemble growth method, where a "population" of samples in the state space is considered, as opposed to traditional sampling by long random walks, or iterative single-chain growth. The second is the flat-histogram Monte Carlo, similar to the popular Wang-Landau sampling, or to multicanonical chain-growth sampling. We discuss the performance and relative simplicity of the proposed algorithm, and we apply it to known test cases.
Collapse
Affiliation(s)
- Graziano Vernizzi
- Department of Physics and Astronomy, Siena College, Loudonville, New York 12211, USA
| | - Trung Dac Nguyen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Henri Orland
- Institut de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.,Beijing Computational Science Research Center, No. 10 East Xibeiwang Road, Beijing 100193, China
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| |
Collapse
|
5
|
Zhang XK, Su JY. Monte Carlo simulation of coil-to-globule transition of compact polymer chains: Role of monomer interacting. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1801002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-ke Zhang
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jia-ye Su
- Department of Applied Physics, Nanjing University of Science and Technology, Nanjing 210094, China
| |
Collapse
|
6
|
Farris ACK, Shi G, Wüst T, Landau DP. The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study. J Chem Phys 2018; 149:125101. [PMID: 30278675 DOI: 10.1063/1.5045482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using Monte Carlo simulations, we investigate simple, physically motivated extensions to the hydrophobic-polar lattice protein model for the small (46 amino acid) protein Crambin. We use two-dimensional replica-exchange Wang-Landau sampling to study the effects of a bond angle stiffness parameter on the folding and uncover a new step in the collapse process for particular values of this stiffness parameter. A physical interpretation of the folding is developed by analysis of changes in structural quantities, and the free energy landscape is explored. For these special values of stiffness, we find non-degenerate ground states, a property that is consistent with behavior of real proteins, and we use these unique ground states to elucidate the formation of native contacts during the folding process. Through this analysis, we conclude that chain-stiffness is particularly influential in the low energy, low temperature regime of the folding process once the lattice protein has partially collapsed.
Collapse
Affiliation(s)
- Alfred C K Farris
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - Guangjie Shi
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich, 8092 Zürich, Switzerland
| | - David P Landau
- Center for Simulational Physics, Department of Physics and Astronomy, The University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
7
|
Pannuzzo M, Tilton RD, Deserno M. Responsive behavior of a branched-chain polymer network: a molecular dynamics study. SOFT MATTER 2018; 14:6485-6495. [PMID: 30043771 DOI: 10.1039/c7sm02096a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Smart polymer hydrogels, which can undergo structural and volume phase transitions in response to external stimuli, have gained much attention for their widespread technological applications. Compared to linear polymers, branched chains offer more extensive opportunities to rationally design functional materials, since they permit more extensive structural tunability-for instance by adjusting the balance between hydrophobic and hydrophilic units, the grafting fraction of backbone monomers, or the side chain length, topology, and solubility. Here we conduct coarse-grained molecular dynamics simulations to assess how well generic physical principles capture this complex interplay of tuning parameters, specifically when building networks from complex branched chains with a hydrophobic backbone. Swollen chains collapse upon reducing side chain solubility, length, and grafting density, but neither the sharpness of this transition nor its dynamic range, if measured via chain extension, depends monotonically on these parameters. Networks comprising such chains are more swollen and exhibit even sharper transitions, but their higher responsiveness goes along with a swelling ratio that falls behind that of single chains.
Collapse
Affiliation(s)
- Martina Pannuzzo
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | | | | |
Collapse
|
8
|
Martins PHL, Plascak JA, Bachmann M. Adsorption of flexible polymer chains on a surface: Effects of different solvent conditions. J Chem Phys 2018; 148:204901. [DOI: 10.1063/1.5027270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- P. H. L. Martins
- Instituto de Física, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil
| | - J. A. Plascak
- Departamento de Física, Centro de Ciências Exatas e da Natureza, CCEN, Universidade Federal da Paraíba, Cidade Universitária, 58051-970 João Pessoa, PB, Brazil
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA
| | - M. Bachmann
- Instituto de Física, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
9
|
Christiansen H, Majumder S, Janke W. Coarsening and aging of lattice polymers: Influence of bond fluctuations. J Chem Phys 2017; 147:094902. [DOI: 10.1063/1.4991667] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Henrik Christiansen
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, 04009 Leipzig, Germany
| | - Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, 04009 Leipzig, Germany
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, 04009 Leipzig, Germany
| |
Collapse
|
10
|
Werlich B, Taylor MP, Shakirov T, Paul W. On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study. Polymers (Basel) 2017; 9:E38. [PMID: 30970714 PMCID: PMC6432196 DOI: 10.3390/polym9020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/17/2017] [Accepted: 01/19/2017] [Indexed: 01/10/2023] Open
Abstract
Local stiffness of polymer chains is instrumental in all structure formation processes of polymers, from crystallization of synthetic polymers to protein folding and DNA compactification. We present Stochastic Approximation Monte Carlo simulations-a type of flat-histogram Monte Carlo method-determining the density of states of a model class of single semi-flexible polymer chains, and, from this, their complete thermodynamic behavior. The chains possess a rich pseudo phase diagram as a function of stiffness and temperature, displaying non-trivial ground-state morphologies. This pseudo phase diagram also depends on chain length. Differences to existing pseudo phase diagrams of semi-flexible chains in the literature emphasize the fact that the mechanism of stiffness creation matters.
Collapse
Affiliation(s)
- Benno Werlich
- Institut für Physik, Martin-Luther-Universität, 06099 Halle, Germany.
| | - Mark P Taylor
- Department of Physics, Hiram College, Hiram, OH 44234, USA.
| | - Timur Shakirov
- Institut für Physik, Martin-Luther-Universität, 06099 Halle, Germany.
| | - Wolfgang Paul
- Institut für Physik, Martin-Luther-Universität, 06099 Halle, Germany.
| |
Collapse
|
11
|
Landsgesell J, Holm C, Smiatek J. Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions. J Chem Theory Comput 2017; 13:852-862. [PMID: 28029786 DOI: 10.1021/acs.jctc.6b00791] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.
Collapse
Affiliation(s)
- Jonas Landsgesell
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart , D-70569 Stuttgart, Germany
| |
Collapse
|
12
|
Williams MJ, Bachmann M. Significance of bending restraints for the stability of helical polymer conformations. Phys Rev E 2016; 93:062501. [PMID: 27415311 DOI: 10.1103/physreve.93.062501] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 01/30/2023]
Abstract
We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.
Collapse
Affiliation(s)
- Matthew J Williams
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Michael Bachmann
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.,Instituto de Física, Universidade Federal de Mato Grosso, Cuiabá (MT), Brazil.,Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte (MG), Brazil
| |
Collapse
|
13
|
Wang Q, Jiang SJ, Jia W, Luo MB. Simulation Study on the Coil-Globule Transition and Surface Adsorption of HP Chains. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201500071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qi Wang
- Department of Physics; Zhejiang University; Hangzhou 310027 China
| | - Si-Jia Jiang
- Department of Physics; Zhejiang University; Hangzhou 310027 China
| | - Wen Jia
- Department of Physics; Zhejiang University; Hangzhou 310027 China
| | - Meng-Bo Luo
- Department of Physics; Zhejiang University; Hangzhou 310027 China
| |
Collapse
|
14
|
Martins PHL, Bachmann M. Interlocking order parameter fluctuations in structural transitions between adsorbed polymer phases. Phys Chem Chem Phys 2016; 18:2143-51. [PMID: 26690091 DOI: 10.1039/c5cp05038c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By means of contact-density chain-growth simulations of a simple coarse-grained lattice model for a polymer grafted at a solid homogeneous substrate, we investigate the complementary behavior of the numbers of surface-monomer and monomer-monomer contacts under various solvent and thermal conditions. This pair of contact numbers represents an appropriate set of order parameters that enables the distinct discrimination of significantly different compact phases of polymer adsorption. Depending on the transition scenario, these order parameters can interlock in perfect cooperation. The analysis helps understand the transitions from compact filmlike adsorbed polymer conformations into layered morphologies and dissolved adsorbed structures, respectively, in more detail.
Collapse
Affiliation(s)
- Paulo H L Martins
- Instituto de Física, Universidade Federal de Mato Grosso, 78060-900 Cuiabá, MT, Brazil.
| | | |
Collapse
|
15
|
Janke W, Paul W. Thermodynamics and structure of macromolecules from flat-histogram Monte Carlo simulations. SOFT MATTER 2016; 12:642-657. [PMID: 26574738 DOI: 10.1039/c5sm01919b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Over the last decade flat-histogram Monte Carlo simulations, especially multi-canonical and Wang-Landau simulations, have emerged as a strong tool to study the statistical mechanics of polymer chains. These investigations have focused on coarse-grained models of polymers on the lattice and in the continuum. Phase diagrams of chains in bulk as well as chains attached to surfaces were studied, for homopolymers as well as for protein-like models. Also, aggregation behavior in solution of these models has been investigated. We will present here the theoretical background for these simulations, explain the algorithms used and discuss their performance and give an overview over the systems studied with these methods in the literature, where we will limit ourselves to studies of coarse-grained model systems. Implementations of these algorithms on parallel computers will be also briefly described. In parallel to the development of these simulation methods, the power of a micro-canonical analysis of such simulations has been recognized, and we present the current state of the art in applying the micro-canonical analysis to phase transitions in nanoscopic polymer systems.
Collapse
Affiliation(s)
- Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, 04009 Leipzig, Germany.
| | | |
Collapse
|
16
|
Koci T, Bachmann M. Confinement effects upon the separation of structural transitions in linear systems with restricted bond fluctuation ranges. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:042142. [PMID: 26565203 DOI: 10.1103/physreve.92.042142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Indexed: 06/05/2023]
Abstract
By means of advanced parallel replica-exchange Monte Carlo methods we examine the influence of elasticity and confinement on the structural transitions of linear systems with restricted bonded interaction. For this purpose, we adopt a model for coarse-grained flexible polymers of finite length in the dilute regime. Hyperphase diagrams are constructed using energy-dependent canonical quantities to demonstrate the effects of the changes in the range of the confined interaction on the liquid and solid structural phases. With increasing bonded interaction range we observe the disappearance of the liquid phase and the fusion of the gas-liquid (or Θ) and the liquid-solid transitions. One of the most remarkable features, the liquid-gas transition, changes from second to first order if the confined interaction range exceeds a threshold that separates polymeric from nonpolymeric systems. The notoriously difficult sampling of the entropically suppressed conformations in the region of very strong first-order transitions is improved by using multiple Gaussian modified ensembles.
Collapse
Affiliation(s)
- Tomas Koci
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Michael Bachmann
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
- Instituto de Física, Universidade Federal de Mato Grosso, Cuiabá (MT), Brazil
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte (MG), Brazil
| |
Collapse
|
17
|
Coil to globule transition of homo- and block-copolymer with different topological constraint and chain stiffness. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5430-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Vogel T, Gross J, Bachmann M. Thermodynamics of the adsorption of flexible polymers on nanowires. J Chem Phys 2015; 142:104901. [DOI: 10.1063/1.4913959] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas Vogel
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Jonathan Gross
- Institut für Theoretische Physik and Centre for Theoretical Sciences (NTZ), Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Michael Bachmann
- Soft Matter Systems Research Group, Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
- Instituto de Física, Universidade Federal de Mato Grosso, 78060-900 Cuiabá , Mato Grosso, Brazil
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
19
|
Wang W, Zhao P, Yang X, Lu ZY. Coil-to-globule transitions of homopolymers and multiblock copolymers. J Chem Phys 2014; 141:244907. [PMID: 25554180 DOI: 10.1063/1.4904888] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Wang
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
| | - Peng Zhao
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
| | - Xi Yang
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
| | - Zhong-Yuan Lu
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, China
| |
Collapse
|
20
|
Luo MB, Ziebarth JD, Wang Y. Interplay of Coil-Globule Transition and Surface Adsorption of a Lattice HP Protein Model. J Phys Chem B 2014; 118:14913-21. [PMID: 25458556 PMCID: PMC4280116 DOI: 10.1021/jp506126d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
An
end-grafted hydrophobic-polar (HP) model protein chain with
alternating H and P monomers is studied to examine interactions between
the critical adsorption transition due to surface attraction and the
collapse transition due to pairwise attractive H–H interactions.
We find that the critical adsorption phenomenon can always be observed;
however, the critical adsorption temperature TCAP is influenced by the attractive H–H interactions
in some cases. When the collapse temperature Tc is lower than TCAP, the critical
adsorption of the HP chain is similar to that of a homopolymer without
intrachain attractions and TCAP remains
unchanged, whereas the collapse transition is suppressed by the adsorption.
In contrast, for cases where Tc is close
to or higher than TCAP, TCAP of the HP chain is increased, indicating that a collapsed
chain is more easily adsorbed on the surface. The strength of the
H–H attraction also influences the statistical size and shape
of the polymer, with strong H–H attractions resulting in adsorbed
and collapsed chains adopting two-dimensional, circular conformations.
Collapse
Affiliation(s)
- Meng-Bo Luo
- Department of Physics, Zhejiang University , Hangzhou 310027, P. R. China
| | - Jesse D Ziebarth
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis , Memphis, Tennessee 38152, United States
| |
Collapse
|
21
|
Shi G, Vogel T, Wüst T, Li YW, Landau DP. Effect of single-site mutations on hydrophobic-polar lattice proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:033307. [PMID: 25314564 DOI: 10.1103/physreve.90.033307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Indexed: 06/04/2023]
Abstract
We developed a heuristic method for determining the ground-state degeneracy of hydrophobic-polar (HP) lattice proteins, based on Wang-Landau and multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific HP proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground-state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the HP sequence have been found. That is, ground-state energies and degeneracies, as well as other thermodynamic and structural quantities, may be either largely unaffected or may change significantly due to mutation.
Collapse
Affiliation(s)
- Guangjie Shi
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| | - Thomas Vogel
- Theoretical Division (T-1), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Thomas Wüst
- Scientific IT Services, ETH Zürich IT Services, 8092 Zürich, Switzerland
| | - Ying Wai Li
- National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David P Landau
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA
| |
Collapse
|
22
|
Li Y, Wüst T, Landau D. Wang–Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.847273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
23
|
Blavatska V, Janke W. Conformational transitions in random heteropolymer models. J Chem Phys 2014; 140:034904. [DOI: 10.1063/1.4849175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
24
|
Wang-Landau and Stochastic Approximation Monte Carlo for Semi-flexible Polymer Chains. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.phpro.2014.08.137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
25
|
Li YW, Wüst T, Landau DP. Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012706. [PMID: 23410358 DOI: 10.1103/physreve.87.012706] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 10/12/2012] [Indexed: 06/01/2023]
Abstract
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are considered with different types of surfaces, each of which attract either all monomers, only hydrophobic (H) monomers, or only polar (P) monomers, respectively. The diversity of folding behavior in dependence of surface strength is discussed. Analyzing the combined patterns of various structural observables, such as, e.g., the derivatives of the numbers of surface contacts, together with the specific heat, we are able to identify generic categories of folding and transition hierarchies. We also infer a connection between these transition categories and the relative surface strengths, i.e., the ratio of the surface attractive strength to the interchain attraction among H monomers. The validity of our proposed classification scheme is reinforced by the analysis of additional benchmark sequences. We thus believe that the folding hierarchies and identification scheme are generic for HP proteins interacting with attractive surfaces, regardless of chain length, sequence, or surface attraction.
Collapse
Affiliation(s)
- Ying Wai Li
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA.
| | | | | |
Collapse
|
26
|
Pattanasiri B, Li YW, Landau DP, Wüst T, Triampo W. Conformational transitions of a confined lattice protein: A Wang-Landau study. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/402/1/012048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
27
|
Tang W, Zhou Q. Finding multiple minimum-energy conformations of the hydrophobic-polar protein model via multidomain sampling. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031909. [PMID: 23030946 DOI: 10.1103/physreve.86.031909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Indexed: 06/01/2023]
Abstract
We demonstrate the efficiency of the multidomain sampler (MDS) in finding multiple distinct global minima and low-energy local minima in the hydrophobic-polar (HP) lattice protein model. Extending the idea of partitioning energy space in the Wang-Landau algorithm, our approach introduces an additional partitioning scheme to divide the protein conformation space into local basins of attraction. This double-partitioning design is very powerful in guiding the sampler to visit the basins of unexplored local minima. An H-residue subchain distance is used to merge the basins of similar local minima into one domain, which increases the diversity among identified minimum-energy conformations. Moreover, a visit-enhancement factor is introduced for long protein chains to facilitate jumps between basins. Results on three benchmark protein sequences reveal that our approach is capable of finding multiple global minima and hundreds of low-energy local minima of great diversity.
Collapse
Affiliation(s)
- Wei Tang
- Department of Materials Science and Engineering, University of California, Los Angeles, California 90095, USA
| | | |
Collapse
|
28
|
Wüst T, Landau DP. Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins. J Chem Phys 2012; 137:064903. [DOI: 10.1063/1.4742969] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
|
29
|
Blavatska V, Janke W. Polymer adsorption on a fractal substrate: Numerical study. J Chem Phys 2012; 136:104907. [DOI: 10.1063/1.3691102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Swetnam A, Brett C, Allen MP. Phase diagrams of knotted and unknotted ring polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:031804. [PMID: 22587116 DOI: 10.1103/physreve.85.031804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Indexed: 05/31/2023]
Abstract
The phase diagram for a lattice ring polymer under applied force, with variable solvent quality, for different topological knot states, is determined for the first time. In addition to eliminating pseudophases where the polymer is flattened into a single layer, it is found that nontrivial knots result in additional pseudophases under tensile force conditions.
Collapse
Affiliation(s)
- Adam Swetnam
- Department of Physics, University of Warwick, Coventry, United Kingdom
| | | | | |
Collapse
|
31
|
Vasilevskaya VV, Ermilov VA. Computer simulation of macromolecular systems with amphiphilic monomer units: Biomimetic models. POLYMER SCIENCE SERIES A 2011. [DOI: 10.1134/s0965545x11090148] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Li YW, Wüst T, Landau DP. Monte Carlo simulations of the HP model (the "Ising model" of protein folding). COMPUTER PHYSICS COMMUNICATIONS 2011; 182:1896-1899. [PMID: 21804642 PMCID: PMC3143505 DOI: 10.1016/j.cpc.2010.12.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to first undergo a collapse "transition" to a globule state followed by a second "transition" into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of "transitions". These transitions depend upon the relative interaction strengths and are largely inaccessible to "standard" Monte Carlo methods.
Collapse
Affiliation(s)
- Ying Wai Li
- Center for Simulational Physics, The University of Georgia, Athens, GA 30602, U.S.A
| | | | | |
Collapse
|
33
|
Gross J, Janke W, Bachmann M. A GPU approach to parallel replica-exchange polymer simulations. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.phpro.2011.05.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
34
|
Blavatska V, Janke W. Shape anisotropy of polymers in disordered environment. J Chem Phys 2010; 133:184903. [DOI: 10.1063/1.3501368] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
35
|
Swetnam AD, Allen MP. Improving the Wang-Landau algorithm for polymers and proteins. J Comput Chem 2010; 32:816-21. [DOI: 10.1002/jcc.21660] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 08/07/2010] [Indexed: 11/09/2022]
|
36
|
Mella M, Izzo L. Structural properties of hydrophilic polymeric chains bearing covalently–linked hydrophobic substituents: Exploring the effects of chain length, fractional loading and hydrophobic interaction strength with coarse grained potentials and Monte Carlo simulations. POLYMER 2010. [DOI: 10.1016/j.polymer.2010.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
37
|
Möddel M, Janke W, Bachmann M. Systematic microcanonical analyses of polymer adsorption transitions. Phys Chem Chem Phys 2010; 12:11548-54. [DOI: 10.1039/c002862b] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
38
|
Blavatska V, Janke W. Polymers in crowded environment under stretching force: Globule-coil transitions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:051805. [PMID: 20364999 DOI: 10.1103/physreve.80.051805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Indexed: 05/29/2023]
Abstract
We study flexible polymer macromolecules in a crowded (porous) environment, modeling them as self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=2,3 . The influence of stretching force on the polymer folding and the properties of globule-coil transitions are analyzed. Applying the pruned-enriched Rosenbluth chain-growth method, we estimate the transition temperature TTheta between collapsed and extended polymer configurations and construct the phase diagrams of the globule-coil coexistence when varying temperature and stretching force. The transition to a completely stretched state, caused by applying force, is discussed as well.
Collapse
Affiliation(s)
- Viktoria Blavatska
- Institut für Theoretische Physik and Centre for Theoretical Sciences (NTZ), Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany.
| | | |
Collapse
|
39
|
Banerji A, Ghosh I. Revisiting the myths of protein interior: studying proteins with mass-fractal hydrophobicity-fractal and polarizability-fractal dimensions. PLoS One 2009; 4:e7361. [PMID: 19834622 PMCID: PMC2760208 DOI: 10.1371/journal.pone.0007361] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 09/09/2009] [Indexed: 11/20/2022] Open
Abstract
A robust marker to describe mass, hydrophobicity and polarizability distribution holds the key to deciphering structural and folding constraints within proteins. Since each of these distributions is inhomogeneous in nature, the construct should be sensitive in describing the patterns therein. We show, for the first time, that the hydrophobicity and polarizability distributions in protein interior follow fractal scaling. It is found that (barring ‘all-α’) all the major structural classes of proteins have an amount of unused hydrophobicity left in them. This amount of untapped hydrophobicity is observed to be greater in thermophilic proteins, than that in their (structurally aligned) mesophilic counterparts. ‘All-β’(thermophilic, mesophilic alike) proteins are found to have maximum amount of unused hydrophobicity, while ‘all-α’ proteins have been found to have minimum polarizability. A non-trivial dependency is observed between dielectric constant and hydrophobicity distributions within (α+β) and ‘all-α’ proteins, whereas absolutely no dependency is found between them in the ‘all-β’ class. This study proves that proteins are not as optimally packed as they are supposed to be. It is also proved that origin of α-helices are possibly not hydrophobic but electrostatic; whereas β-sheets are predominantly hydrophobic in nature. Significance of this study lies in protein engineering studies; because it quantifies the extent of packing that ensures protein functionality. It shows that myths regarding protein interior organization might obfuscate our knowledge of actual reality. However, if the later is studied with a robust marker of strong mathematical basis, unknown correlations can still be unearthed; which help us to understand the nature of hydrophobicity, causality behind protein folding, and the importance of anisotropic electrostatics in stabilizing a highly complex structure named ‘proteins’.
Collapse
Affiliation(s)
| | - Indira Ghosh
- School of Information Technology, Jawaharlal Nehru University, New Delhi, India
- * E-mail:
| |
Collapse
|
40
|
Vogel T, Neuhaus T, Bachmann M, Janke W. Thermodynamics of tubelike flexible polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:011802. [PMID: 19658721 DOI: 10.1103/physreve.80.011802] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Indexed: 05/28/2023]
Abstract
In this work, we discuss the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling methods to simulate small bead-stick polymer models with Lennard-Jones interaction among nonbonded monomers. We analyze energetic fluctuations and structural quantities to classify conformational pseudophases. We find that the tube thickness influences the thermodynamic behavior of simple tubelike polymers significantly, i.e., for a given temperature, the formation of secondary structures strongly depends on the tube thickness.
Collapse
Affiliation(s)
- Thomas Vogel
- Institut für Theoretische Physik and Centre for Theoretical Sciences (NTZ), Universität Leipzig, Postfach 100 920, 04009 Leipzig, Germany
| | | | | | | |
Collapse
|
41
|
Wüst T, Landau DP. Versatile approach to access the low temperature thermodynamics of lattice polymers and proteins. PHYSICAL REVIEW LETTERS 2009; 102:178101. [PMID: 19518836 DOI: 10.1103/physrevlett.102.178101] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Indexed: 05/27/2023]
Abstract
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and the interacting self-avoiding walk (ISAW) model for homopolymers. We obtain accurate estimates of thermodynamic quantities for HP sequences with >100 monomers and for ISAWs up to >500 monomers. Our procedure possesses an intrinsic simplicity and overcomes the limitations inherent in more tailored approaches making it interesting for a broad range of protein and polymer models.
Collapse
Affiliation(s)
- Thomas Wüst
- Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.
| | | |
Collapse
|
42
|
Sharma S, Kumar SK. Finite size effects on locating conformational transitions for macromolecules. J Chem Phys 2009; 129:134901. [PMID: 19045121 DOI: 10.1063/1.2979142] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been shown from simulation and experiment that locations of peaks in structural and thermodynamic quantities accompanying "phase" transitions of a single macromolecule (collapse or crystallization/melting) do not coincide. Thus, for chains with finite lengths these different measures yield apparently different results for transition temperatures. To resolve this issue we use scaling, verified by computer simulations, to conclusively show that these different locations for peak positions are simply a consequence of the finite chain length, as has been conjectured previously.
Collapse
Affiliation(s)
- Sumit Sharma
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
| | | |
Collapse
|
43
|
Swetnam AD, Allen MP. Improved simulations of lattice peptide adsorption. Phys Chem Chem Phys 2009; 11:2046-55. [DOI: 10.1039/b818067a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
44
|
Schluttig J, Bachmann M, Janke W. Comparative molecular dynamics and Monte Carlo study of statistical properties for coarse-grained heteropolymers. J Comput Chem 2008; 29:2603-12. [PMID: 18478584 DOI: 10.1002/jcc.21003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Employing a simple hydrophobic-polar heteropolymer model, we compare thermodynamic quantities obtained from Andersen and Nosé-Hoover molecular dynamics as well as replica-exchange Monte Carlo methods. We find qualitative correspondence in the results, but serious quantitative differences using the Nosé-Hoover chain thermostat. For analyzing the deviations, we study different parameterizations of the Nosé-Hoover chain thermostat. Autocorrelations from molecular dynamics and Metropolis Monte Carlo runs are also investigated.
Collapse
Affiliation(s)
- Jakob Schluttig
- Institut für Theoretische Physik and Centre for Theoretical Sciences (NTZ), Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany
| | | | | |
Collapse
|
45
|
Arkin H. Determination of the structure of the energy landscape for coarse-grained off-lattice models of folding heteropolymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:041914. [PMID: 18999462 DOI: 10.1103/physreve.78.041914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 08/21/2008] [Indexed: 05/27/2023]
Abstract
The structure of energy landscapes for a minimalist coarse-grained off-lattice protein model is presented to investigate the folding behaviors of heteropolymers. The obtained energy landscapes serve as a useful tool for visualization of the funnel-like structure of a considered system in the configuration space. Despite the simplicity of the model, the knowledge of the free-energy landscape enables us to show different folding characteristics known from real proteins and synthetic peptides, such as two-state folding and metastability.
Collapse
Affiliation(s)
- Handan Arkin
- Faculty of Engineering, Department of Physics Engineering Tandoğan, Ankara University, Ankara, Turkey.
| |
Collapse
|
46
|
Binder K, Paul W. Recent Developments in Monte Carlo Simulations of Lattice Models for Polymer Systems. Macromolecules 2008. [DOI: 10.1021/ma702843z] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. Binder
- Institut für Physik, Johannes Gutenberg-Universität, Staudinger Weg 7, D-55099 Mainz, Germany
| | - W. Paul
- Institut für Physik, Johannes Gutenberg-Universität, Staudinger Weg 7, D-55099 Mainz, Germany
| |
Collapse
|
47
|
Junghans C, Bachmann M, Janke W. Thermodynamics of peptide aggregation processes: an analysis from perspectives of three statistical ensembles. J Chem Phys 2008; 128:085103. [PMID: 18315086 DOI: 10.1063/1.2830233] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We employ a mesoscopic model for studying aggregation processes of proteinlike hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to non-negligible surface effects of the small systems. We analyze thermodynamic properties of the conformational transitions accompanying the aggregation process from the multicanonical, canonical, and microcanonical perspective. It turns out that the microcanonical description is particularly advantageous as it allows for unraveling details of the phase-separation transition in the thermodynamic region, where the temperature is not a suitable external control parameter anymore.
Collapse
Affiliation(s)
- Christoph Junghans
- Institut für Theoretische Physik and Centre for Theoretical Sciences NTZ, Universität Leipzig, Postfach 100920, D-04009 Leipzig, Germany.
| | | | | |
Collapse
|
48
|
Vogel T, Bachmann M, Janke W. Freezing and collapse of flexible polymers on regular lattices in three dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:061803. [PMID: 18233861 DOI: 10.1103/physreve.76.061803] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Indexed: 05/25/2023]
Abstract
We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple-cubic and face-centered-cubic lattices by means of sophisticated chain-growth methods. In contrast to the bond-fluctuation polymer model in certain parameter ranges, where these two conformational transitions were found to merge in the thermodynamic limit, we conclude from our results that the two transitions remain well separated in the limit of infinite chain lengths. The reason for this qualitatively distinct behavior is presumably due to the ultrashort attractive interaction range in the lattice models considered here.
Collapse
Affiliation(s)
- Thomas Vogel
- Institut für Theoretische Physik, Universität Leipzig, Postfach 100 920, D-04009 Leipzig, Germany.
| | | | | |
Collapse
|
49
|
Patel BA, Debenedetti PG, Stillinger FH. Method for Efficient Computation of the Density of States in Water-Explicit Biopolymer Simulations on a Lattice. J Phys Chem A 2007; 111:12651-8. [DOI: 10.1021/jp0761970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bryan A. Patel
- Department of Chemical Engineering, and Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Pablo G. Debenedetti
- Department of Chemical Engineering, and Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| | - Frank H. Stillinger
- Department of Chemical Engineering, and Department of Chemistry, Princeton University, Princeton, New Jersey 08544
| |
Collapse
|
50
|
Zhang J, Kou SC, Liu JS. Biopolymer structure simulation and optimization via fragment regrowth Monte Carlo. J Chem Phys 2007; 126:225101. [PMID: 17581081 DOI: 10.1063/1.2736681] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient exploration of the configuration space of a biopolymer is essential for its structure modeling and prediction. In this study, the authors propose a new Monte Carlo method, fragment regrowth via energy-guided sequential sampling (FRESS), which incorporates the idea of multigrid Monte Carlo into the framework of configurational-bias Monte Carlo and is suitable for chain polymer simulations. As a by-product, the authors also found a novel extension of the Metropolis Monte Carlo framework applicable to all Monte Carlo computations. They tested FRESS on hydrophobic-hydrophilic (HP) protein folding models in both two and three dimensions. For the benchmark sequences, FRESS not only found all the minimum energies obtained by previous studies with substantially less computation time but also found new lower energies for all the three-dimensional HP models with sequence length longer than 80 residues.
Collapse
Affiliation(s)
- Jinfeng Zhang
- Department of Statistics, Harvard University, Science Center, Cambridge, Massachusetts 02138, USA
| | | | | |
Collapse
|