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Xu X, Xiao X, Xu S, Liu H. Computational insights into the destabilization of α-helical conformations formed by leucine zipper peptides in response to temperature. Phys Chem Chem Phys 2018; 18:25465-25473. [PMID: 27722604 DOI: 10.1039/c6cp05145f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent experiments in our lab (Phys. Chem. Chem. Phys., 2016, 18, 10129-10137) suggested using leucine zipper peptides to enhance the thermosensitivity of liposomes. To understand the mechanisms of temperature-responsive control by the leucine zipper peptide in liposomes, we firstly performed quantum mechanics calculations and implicit-solvent replica exchange molecular dynamics simulations to study the thermo-stability of two leucine zipper peptides, CH3(CH2)4-CO-[VAQLEVK-VAQLESK-VSKLESK-VSSLESK] (termed the capped peptide) and A-[VAQLEVK-VAQLESK-VSKLESK-VSSLESK] (termed the ALA peptide). The analysis of dihedral angle principal components and protein secondary structures was conducted to determine the temperature-dependence conformation transition of the two peptides. Simulation results revealed that our computed transition temperature of the capped peptide is 319.1 K that accords with experimental measurement, 321.1 K. Later, explicit-solvent conventional molecular dynamics simulations were carried out to examine the process of folding and unfolding of the ALA and capped peptides complexed with a lipid bilayer and water in the vicinity of their transition temperatures. A further analysis of conformation and energy of the folded peptides showed that the increase of temperature gives rise to a notable decrease in the number of intra-chain hydrogen bonds and a significant increase in the potential energy of the peptides, thereby reducing the folding stability of the two peptides. As compared to the ALA peptide, a lower transition temperature caused by less intra-chain hydrogen bonds was observed in the capped peptide, which is closer to the temperature of tumor cells. This fact suggests that the capped peptide is more suitable to produce highly sensitive liposomes for the delivery of cancer drugs.
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Affiliation(s)
- Xiejun Xu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Shouhong Xu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Honglai Liu
- State Key Laboratory of Chemical Engineering and School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
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Shuaib S, Goyal B. Scrutiny of the mechanism of small molecule inhibitor preventing conformational transition of amyloid-β 42 monomer: insights from molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:663-678. [PMID: 28162045 DOI: 10.1080/07391102.2017.1291363] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that is characterized by loss of intellectual functioning of brain and memory loss. According to amyloid cascade hypothesis, aggregation of amyloid-β42 (Aβ42) peptide can generate toxic oligomers and their accumulation in the brain is responsible for the onset of AD. In spite of carrying out a large number of experimental studies on inhibition of Aβ42 aggregation by small molecules, the detailed inhibitory mechanism remains elusive. In the present study, comparable molecular dynamics (MD) simulations were performed to elucidate the inhibitory mechanism of a sulfonamide inhibitor C1 (2,5-dichloro-N-(4-piperidinophenyl)-3-thiophenesulfonamide), reported for its in vitro and in vivo anti-aggregation activity against Aβ42. MD simulations reveal that C1 stabilizes native α-helix conformation of Aβ42 by interacting with key residues in the central helix region (13-26) with hydrogen bonds and π-π interactions. C1 lowers the solvent-accessible surface area of the central hydrophobic core (CHC), KLVFF (16-20), that confirms burial of hydrophobic residues leading to the dominance of helical conformation in the CHC region. The binding free energy analysis with MM-PBSA demonstrates that Ala2, Phe4, Tyr10, Gln15, Lys16, Leu17, Val18, Phe19, Phe20, Glu22, and Met35 contribute maximum to binding free energy (-43.1 kcal/mol) between C1 and Aβ42 monomer. Overall, MD simulations reveal that C1 inhibits Aβ42 aggregation by stabilizing native helical conformation and inhibiting the formation of aggregation-prone β-sheet conformation. The present results will shed light on the underlying inhibitory mechanism of small molecules that show potential in vitro anti-aggregation activity against Aβ42.
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Affiliation(s)
- Suniba Shuaib
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
| | - Bhupesh Goyal
- a Department of Chemistry , School of Basic and Applied Sciences, Sri Guru Granth Sahib World University , Fatehgarh Sahib 140406 , Punjab , India
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Goyal B, Kumar A, Srivastava KR, Durani S. Scrutiny of chain-length and N-terminal effects in α-helix folding: a molecular dynamics study on polyalanine peptides. J Biomol Struct Dyn 2016; 35:1923-1935. [DOI: 10.1080/07391102.2016.1199972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:463-82. [DOI: 10.1007/s00249-016-1115-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
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6
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A compact native 24-residue supersecondary structure derived from the villin headpiece subdomain. Biophys J 2015; 108:678-86. [PMID: 25650934 DOI: 10.1016/j.bpj.2014.11.3482] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 11/20/2014] [Indexed: 11/22/2022] Open
Abstract
Many small proteins fold highly cooperatively in an all-or-none fashion and thus their native states are well protected from thermal fluctuations by an extensive network of interactions across the folded structure. Because protein structures are stabilized by local and nonlocal interactions among distal residues, dissecting individual substructures from the context of folded proteins results in large destabilization and loss of unique three-dimensional structure. Thus, mini-protein substructures can only rarely be derived from natural templates. Here, we describe a compact native 24-residues-long supersecondary structure derived from the hyperstable villin headpiece subdomain consisting of helices 2 and 3 (HP24). Using a combination of experimental techniques, including NMR and small-angle x-ray scattering, as well as all-atom replica exchange molecular-dynamics simulations, we show that a variant with stabilizing substitutions (HP24stab) forms a densely packed and compact conformation. In HP24stab, interactions between helices 2 and 3 are similar to those observed in native folded HP35, and the two helices cooperatively stabilize each other by completing the hydrophobic core lining the central part of HP35. Interestingly, even though the HP24wt fragment shows a more expanded and less structured conformation, NMR and simulations demonstrate a preference for a native-like topology. Thus, the two stabilizing residues in HP24stab shift the energy balance toward the native state, leading to a minimal folding motif.
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Haque MA, Zaidi S, Ubaid-ullah S, Prakash A, Hassan MI, Islam A, Batra JK, Ahmad F. In vitro and in silico studies of urea-induced denaturation of yeast iso-1-cytochromecand its deletants at pH 6.0 and 25 °C. J Biomol Struct Dyn 2014; 33:1493-502. [DOI: 10.1080/07391102.2014.958760] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain. J Mol Model 2014; 20:2283. [PMID: 24863533 DOI: 10.1007/s00894-014-2283-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/25/2014] [Indexed: 10/25/2022]
Abstract
Proteins fold by diverse pathways which depend on the energy barriers involved in reaching different intermediates. There has been a lot of development in the theoretical aspects of protein folding, from force-field to simulation techniques. One such simulation approach is replica exchange molecular dynamics simulation (REMD), which provides an efficient conformational sampling method to understand the events involved in protein folding. In this study, an attempt is made to explore the folding funnel of engrailed homeodomain protein (EnHD) using REMD simulations. EnHD is a 54 residue long helix bundle protein which has a folding time of about 15 μs. The protein was represented using the Amber United atom model in order to reduce the system size which helped to speed up the simulation. Individual replicas were simulated for 1.4-2 μs making cumulative time of more than 100 μs of REMD simulations. Free energy analysis was carried out to understand the folding behavior of EnHD protein. Effects of temperature range and exchange frequency in REMD simulations have been explored. In addition to this, multiple umbrella sampling (US) simulations of a total of 320 ns were also carried out, followed by weighted histogram analysis method (WHAM) to investigate the energy barriers involved during the folding of various intermediates. US studies were also carried on mutational variants of EnHD protein to see effect of the mutations on the folding pathway of the protein. The use of US technique may be helpful for predicting fast folding mutants or protein engineering. The combination of REMD with US may help in understanding the energetics between multiple pathways of fast folding proteins and their mutant counterparts.
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Duan LL, Zhu T, Zhang QG, Tang B, Zhang JZH. Electronic polarization stabilizes tertiary structure prediction of HP-36. J Mol Model 2014; 20:2195. [PMID: 24715046 PMCID: PMC3996369 DOI: 10.1007/s00894-014-2195-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 03/02/2014] [Indexed: 01/10/2023]
Abstract
Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.
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Affiliation(s)
- Li L Duan
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
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10
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Ultrafast folding kinetics and cooperativity of villin headpiece in single-molecule force spectroscopy. Proc Natl Acad Sci U S A 2013; 110:18156-61. [PMID: 24145407 DOI: 10.1073/pnas.1311495110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In this study we expand the accessible dynamic range of single-molecule force spectroscopy by optical tweezers to the microsecond range by fast sampling. We are able to investigate a single molecule for up to 15 min and with 300-kHz bandwidth as the protein undergoes tens of millions of folding/unfolding transitions. Using equilibrium analysis and autocorrelation analysis of the time traces, the full energetics as well as real-time kinetics of the ultrafast folding of villin headpiece 35 and a stable asparagine 68 alanine/lysine 70 methionine variant can be measured directly. We also performed Brownian dynamics simulations of the response of the bead-DNA system to protein-folding fluctuations. All key features of the force-dependent deflection fluctuations could be reproduced: SD, skewness, and autocorrelation function. Our measurements reveal a difference in folding pathway and cooperativity between wild-type and stable variant of headpiece 35. Autocorrelation force spectroscopy pushes the time resolution of single-molecule force spectroscopy to ∼10 µs thus approaching the timescales accessible for all atom molecular dynamics simulations.
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Chen Y, Ding J. Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation. J Biomol Struct Dyn 2013; 32:792-803. [PMID: 23746129 DOI: 10.1080/07391102.2013.791645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56 Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.
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Affiliation(s)
- Yantao Chen
- a State Key Laboratory of Molecular Engineering of Polymers, Shenzhen Key Laboratory of Functional Polymer , College of Chemistry and Chemical Engineering, Shenzhen University , Shenzhen , 518060 , China
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Chang S, He HQ, Hu JP, Jiao X, Tian XH. Network models reveal stability and structural rearrangement of signal recognition particle. J Biomol Struct Dyn 2012; 30:150-9. [PMID: 22702726 DOI: 10.1080/07391102.2012.677765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The signal recognition particle (SRP) and its receptors (SR) mediate the cotranslational targeting of the membrane and secretory proteins in all cells. In Escherichia coli, SRP is composed of the Ffh protein and the 4.5S SRP RNA. Ffh is a multidomain protein comprising a methionine-rich (M) domain, a helical N domain, and a Ras-like guanine triphosphatase (GTPase) (G) domain. The N and G domains are commonly referred to as one structural unit, the NG domain. In this article, the complex structure of SRP and SR is investigated with the Gaussian network model (GNM) and anisotropic network model (ANM). GNM provides the information of structure stability. It is found that the intermolecular interactions between SRP and SR can obviously decrease the fluctuation of NG domains. Nevertheless, the large structural rearrangement will take place during the cotranslational protein targeting cycle. Hence, the moving directions of fluctuation regions are further ascertained by using cross-correlation analysis and the ANM. The NG domain of Ffh undergoes a clockwise rotation around the GM linker and the M domain of Ffh shows an opposite direction to the NG domain. These functional movements will facilitate the SRP structure to transform into the free form and the sequence-bound form. These simple coarse-grained analyses can be used as a general and quick method for the mechanism studies of protein assembly and supramolecular systems.
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Affiliation(s)
- Shan Chang
- College of Informatics, South China Agricultural University, Guangzhou, 510642, China.
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Wang ZJ, Si YX, Oh S, Yang JM, Yin SJ, Park YD, Lee J, Qian GY. The effect of fucoidan on tyrosinase: computational molecular dynamics integrating inhibition kinetics. J Biomol Struct Dyn 2012; 30:460-73. [PMID: 22694253 DOI: 10.1080/07391102.2012.682211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fucoidan is a complex sulfated polysaccharide extracted from brown seaweed and has a wide variety of biological activities. In this study, we investigated the inhibitory effect of fucoidan on tyrosinase via a combination of inhibition kinetics and computational simulations. Fucoidan reversibly inhibited tyrosinase in a mixed-type manner. Time-interval kinetics showed that the inhibition was processed as first order with biphasic processes. For further insight, we simulated dockings with various sizes of molecular models (monomer to decamer) of fucoidan and showed that the best binding energy change results were obtained from the pentamer (-1.89 kcal/mol) and the hexamer (-1.97 kcal/mol) models of AutoDock Vina. The molecular dynamics simulation confirmed the binding mechanisms between tyrosinase and fucoidan and suggested that fucoidan mostly interacts with several residues including copper ions located in the active site. Our study suggests that fucoidan might be a potential natural antipigment agent.
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Affiliation(s)
- Zhi-Jiang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, P.R. China
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Majumder R, Roy S, Thakur AR. Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies. J Biomol Struct Dyn 2012; 30:13-29. [DOI: 10.1080/07391102.2012.674184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Hamza A, Wei NN, Johnson-Scalise T, Naftolin F, Cho H, Zhan CG. Unveiling the Unfolding Pathway of F5F8D Disorder-Associated D81H/V100D Mutant of MCFD2viaMultiple Molecular Dynamics Simulations. J Biomol Struct Dyn 2012; 29:699-714. [DOI: 10.1080/07391102.2012.10507410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Ramakrishnan V, Jagannathan S, Shaikh AR, Rajagopalan R. Dynamic and Structural Changes in the Minimally Restructuring EcoRI Bound to a Minimally Mutated DNA Chain. J Biomol Struct Dyn 2012; 29:743-56. [DOI: 10.1080/073911012010525020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Cao Z, Liu L, Wang J. Why the OPLS-AA Force Field Cannot Produce the β-Hairpin Structure of H1 Peptide in Solution When Comparing with the GROMOS 43A1 Force Field? J Biomol Struct Dyn 2011; 29:527-39. [DOI: 10.1080/07391102.2011.10507403] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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