Polymer folding via external potentials in ab-initio calculations
[Display omitted] •External potentials in ab-initio calculations can induce the folding of polymers.•A general Langevin equation of motion is deduced with an external potential.•The results of a model polymer are in agreement with molecular mechanics.•The approach shows great promises for investigat...
Saved in:
| Published in | Computational and theoretical chemistry Vol. 1068; pp. 72 - 80 |
|---|---|
| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Elsevier B.V
15.09.2015
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 2210-271X |
| DOI | 10.1016/j.comptc.2015.06.012 |
Cover
Loading…
| Abstract | [Display omitted]
•External potentials in ab-initio calculations can induce the folding of polymers.•A general Langevin equation of motion is deduced with an external potential.•The results of a model polymer are in agreement with molecular mechanics.•The approach shows great promises for investigating the folding of proteins.•The approach is compatible with the new computer technologies.
A general method based on the Zwanzig–Langevin approach is provided to investigate the folding of biological or synthetic polymers. The method departs from a Lagrangian for a molecule inside a fluid (liquid or gas), and subject to an external potential. The equations of motion are deduced and solved by considering the statistical nature of the fluid. We study different external potentials capable of inducing the folding. The results on a model polymer (polyethylene) are very promising since several minima close in energy are distinguished for very different molecular conformations. The external potentials not only facilitate the folding, but also provide an alternative for rapidly determining the energetically stable structures. |
|---|---|
| AbstractList | [Display omitted]
•External potentials in ab-initio calculations can induce the folding of polymers.•A general Langevin equation of motion is deduced with an external potential.•The results of a model polymer are in agreement with molecular mechanics.•The approach shows great promises for investigating the folding of proteins.•The approach is compatible with the new computer technologies.
A general method based on the Zwanzig–Langevin approach is provided to investigate the folding of biological or synthetic polymers. The method departs from a Lagrangian for a molecule inside a fluid (liquid or gas), and subject to an external potential. The equations of motion are deduced and solved by considering the statistical nature of the fluid. We study different external potentials capable of inducing the folding. The results on a model polymer (polyethylene) are very promising since several minima close in energy are distinguished for very different molecular conformations. The external potentials not only facilitate the folding, but also provide an alternative for rapidly determining the energetically stable structures. |
| Author | González-García, Tania Santamaria, Ruben Jones, Keith Arroyo, Maricela |
| Author_xml | – sequence: 1 givenname: Ruben surname: Santamaria fullname: Santamaria, Ruben email: rso@fisica.unam.mx organization: Dept. de Física Teórica, Instituto de Física, UNAM, D.F. 01000, Mexico – sequence: 2 givenname: Keith surname: Jones fullname: Jones, Keith email: joneska@email.arizona.edu organization: Dept. of Chemistry & Biochemistry, University of Arizona, Tucson, AZ 85721, United States – sequence: 3 givenname: Maricela surname: Arroyo fullname: Arroyo, Maricela email: m.arroyo@correo.ler.uam.mx organization: Depto. Procesos Productivos, Universidad Autónoma Metropolitana, Unidad Lerma, Av. Hidalgo Poniente 46, Col. La Estación, CP. 52006 Lerma de Villada, Mexico – sequence: 4 givenname: Tania surname: González-García fullname: González-García, Tania email: taniaglz@fisica.unam.mx organization: Dept. de Física Teórica, Instituto de Física, UNAM, D.F. 01000, Mexico |
| BookMark | eNqFj89OwzAMh3MYEgP2Bhz6Ai1x0qYdB6Rp4p80CQ4gcYtSx0WZumRKw8Teno5x4gC-2JL9_eTvjE188MTYJfACOKirdYFhs01YCA5VwVXBQUzYVAjguajh7ZTNhmHNxyqVHHdTtngO_X5DMetCb51_z3bOZPSZKHrTZ9uQyCdn-iFzPjNt7rxLLmRoevzozTj64YKddOMBzX76OXu9u31ZPuSrp_vH5WKVo-Qq5UBQ2nqOvIOOqq5VQCXOpbJVLUBK4HZuBbayaS3UWJsKGyGh4ZUwolLQyHNWHnMxhmGI1OltdBsT9xq4PtjrtT7a64O95kqPhiN2_QtDl74_T9G4_j_45gjTKLZzFPWAjjySdZEwaRvc3wFf_El8iQ |
| CitedBy_id | crossref_primary_10_1007_s10955_016_1569_x crossref_primary_10_1016_j_comptc_2016_11_021 crossref_primary_10_1016_j_compbiolchem_2020_107262 |
| Cites_doi | 10.1016/S0959-440X(00)00194-9 10.1016/S0301-0104(98)00214-6 10.1080/00268978200100491 10.1002/jcc.540141112 10.1016/j.sbi.2004.01.009 10.1021/ct300709u 10.1063/1.4891807 10.1063/1.476053 10.1016/j.jbbm.2007.10.006 10.1080/21553769.2013.776995 10.1088/0034-4885/29/1/306 10.1103/PhysRevB.37.785 10.1016/j.bbrc.2008.12.099 10.1103/PhysRevE.56.5018 10.1006/jcph.1999.6218 10.1103/PhysRevLett.56.930 10.1103/PhysRevE.84.041934 10.1063/1.1679979 10.1021/jp8106793 10.1103/PhysRevLett.78.2690 10.1063/1.3382344 10.1021/ct9003004 10.1021/jp4121854 10.1007/BF01008729 10.1021/ct100320g 10.1016/S1093-3263(00)00133-9 10.1103/RevModPhys.15.1 10.1063/1.1651473 10.1016/j.cpc.2010.04.018 10.1038/nrm3658 10.1016/j.jtice.2011.03.003 10.1021/ar970083x 10.1063/1.4725183 10.1016/j.bpj.2011.05.010 10.1103/PhysRevA.38.3098 10.3390/ijms10030889 10.1038/387308a0 10.1126/science.3547653 10.3390/ijms10041719 |
| ContentType | Journal Article |
| Copyright | 2015 Elsevier B.V. |
| Copyright_xml | – notice: 2015 Elsevier B.V. |
| DBID | AAYXX CITATION |
| DOI | 10.1016/j.comptc.2015.06.012 |
| DatabaseName | CrossRef |
| DatabaseTitle | CrossRef |
| DatabaseTitleList | |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Chemistry |
| EndPage | 80 |
| ExternalDocumentID | 10_1016_j_comptc_2015_06_012 S2210271X15002443 |
| GroupedDBID | --K --M .~1 0R~ 1~. 1~5 4.4 457 4G. 5VS 7-5 8P~ AACTN AAEDT AAEDW AAIAV AAIKJ AAKOC AALRI AAOAW AAQFI AARLI AAXUO ABFRF ABJNI ABMAC ABNEU ABYKQ ACDAQ ACFVG ACGFO ACGFS ACRLP ADBBV ADECG ADEZE AEBSH AEFWE AEKER AENEX AFKWA AFTJW AFZHZ AGHFR AGUBO AGYEJ AIEXJ AIKHN AITUG AIVDX AJBFU AJOXV AJSZI ALMA_UNASSIGNED_HOLDINGS AMFUW AMRAJ AXJTR BKOJK BLXMC EBS EFJIC EFLBG EJD FDB FIRID FLBIZ FNPLU FYGXN GBLVA J1W KOM M41 MO0 O-L O9- OAUVE OGIMB P-8 P-9 PC. Q38 RIG RNS ROL SDF SES SPC SPCBC SSK SSQ SSZ T5K ~G- AATTM AAXKI AAYWO AAYXX ABWVN ABXDB ACNNM ACRPL ACVFH ADCNI ADMUD ADNMO AEIPS AEUPX AFJKZ AFPUW AFXIZ AGCQF AGRNS AIGII AIIUN AKBMS AKRWK AKYEP ANKPU APXCP BNPGV CITATION HZ~ SSH |
| ID | FETCH-LOGICAL-c306t-1e14d79c0f1fe5fb61e4c936d57213310d9d2cb38bd17c7a5c82318052a256183 |
| IEDL.DBID | .~1 |
| ISSN | 2210-271X |
| IngestDate | Tue Jul 01 02:16:01 EDT 2025 Thu Apr 24 22:54:16 EDT 2025 Fri Feb 23 02:22:05 EST 2024 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Keywords | Molecular dynamics Density functional theory External potentials Polymer folding |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c306t-1e14d79c0f1fe5fb61e4c936d57213310d9d2cb38bd17c7a5c82318052a256183 |
| PageCount | 9 |
| ParticipantIDs | crossref_primary_10_1016_j_comptc_2015_06_012 crossref_citationtrail_10_1016_j_comptc_2015_06_012 elsevier_sciencedirect_doi_10_1016_j_comptc_2015_06_012 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2015-09-15 |
| PublicationDateYYYYMMDD | 2015-09-15 |
| PublicationDate_xml | – month: 09 year: 2015 text: 2015-09-15 day: 15 |
| PublicationDecade | 2010 |
| PublicationTitle | Computational and theoretical chemistry |
| PublicationYear | 2015 |
| Publisher | Elsevier B.V |
| Publisher_xml | – name: Elsevier B.V |
| References | Tskhovrebova, Trinick, Sleep, Simmons (b0045) 1997; 387 Goldstein (b0190) 1980 D. van der Spoel, E. Lindahl, B. Hess, The GROMACS development team, GROMACS user manual, version 4.6.5, 2013. Ponmurugan, Vemparala (b0120) 2012; 6 Chandrasekhar (b0215) 1943; 15 Ozer, Quirk, Hernández (b0130) 2012; 8 Roy, Goedecker, Field, Penev (b0065) 2009; 113 Ufimtsev, Martinez (b0235) 2009; 5 Isralewitz, Gao, Schulten (b0110) 2001; 11 Ashkin, Dziedzic (b0035) 1987; 235 Liu, Wang, Jiang (b0145) 2008; 70 Lee, Yang, Parr (b0225) 1988; 37 . Szilágyi, Kardos, Osváth, Barna, Závodszky (b0015) 2007 Gullingsrud, Braun, Schulten (b0070) 1999; 151 Onuchic, Wolynes (b0010) 2004; 14 Wang, Su (b0090) 2011; 42 Becke (b0220) 1988; 138 Park, Schulten (b0075) 2004; 120 Ehrenstein (b0050) 2001 Jarzynski (b0085) 1997; 56 van Gunsteren, Berendsen (b0200) 1982; 45 Schmidt, Baldridge, Boatz, Elbert, Gordon, Jensen, Koseki, Matsunaga, Nguyen, Su, Windus, Dupuis, Montgomery (b0245) 1993; 14 Ruben Santamaria, Zwanzig–Langevin molecular dynamics software code, 2014. Isralewitz, Gao, Schulten (b0020) 2001; 11 Zwanzig (b0185) 1973; 9 Germana Paterlini, Ferguson (b0205) 1998; 236 Gruebele, Sabelko, Ballew, Ervin (b0040) 1998; 31 Kubo (b0210) 1966; 29-1 Santamaria, Adamowicz, Rosas-Acevedo (b0180) 2014 Ozer, Quirk, Hernandez (b0135) 2012; 136 Liu, Hsin, Kim, Selvin, Schulten (b0100) 2011; 100 Grimme, Antony, Ehrlich, Krieg (b0230) 2010; 132 Ozer, Valeev, Quirk, Hernandez (b0125) 2010; 6 Ozer, Keyes, Quirk, Hernandez (b0140) 2014; 141 Gutin, Sali, Abkevich, Karplus, Shakhnovich (b0155) 1998; 108 Byrd, Bartlett, Montgomery (b0165) 2014; 118 Eddington (b0195) 1928 Watson, Baker, Bell, Gann, Levine, Losick (b0005) 2014 Isralewitz, Baudry, Gullingsrud, Kosztin, Schulten (b0115) 2001; 19 Binning, Quate, Gerber (b0030) 1986; 56 Valiev, Bylaska, Govind, Kowalski, Straatsma, Van Dam, Wang, Nieplocha, Apra, Windus, de Jong (b0240) 2010; 181 Su, Wang (b0105) 2009; 10 Wolff, Vendruscolo, Porto (b0055) 2011; 84 Saibil (b0170) 2013; 14 Verdier (b0160) 1973; 59 Lu, Schulten (b0025) 1999; 35 Yang, Liu, Wang, Jiang (b0150) 2008; 379 Hills, Brooks (b0060) 2009; 10 Jarzynski (b0080) 1997; 78 Lu, Schulten (b0095) 1999; 35 Malpass (b0175) 2010 Ozer (10.1016/j.comptc.2015.06.012_b0130) 2012; 8 Saibil (10.1016/j.comptc.2015.06.012_b0170) 2013; 14 Lu (10.1016/j.comptc.2015.06.012_b0095) 1999; 35 Tskhovrebova (10.1016/j.comptc.2015.06.012_b0045) 1997; 387 Yang (10.1016/j.comptc.2015.06.012_b0150) 2008; 379 Isralewitz (10.1016/j.comptc.2015.06.012_b0115) 2001; 19 Verdier (10.1016/j.comptc.2015.06.012_b0160) 1973; 59 Park (10.1016/j.comptc.2015.06.012_b0075) 2004; 120 Liu (10.1016/j.comptc.2015.06.012_b0145) 2008; 70 Zwanzig (10.1016/j.comptc.2015.06.012_b0185) 1973; 9 10.1016/j.comptc.2015.06.012_b0250 Gruebele (10.1016/j.comptc.2015.06.012_b0040) 1998; 31 10.1016/j.comptc.2015.06.012_b0255 Hills (10.1016/j.comptc.2015.06.012_b0060) 2009; 10 Eddington (10.1016/j.comptc.2015.06.012_b0195) 1928 Liu (10.1016/j.comptc.2015.06.012_b0100) 2011; 100 Gullingsrud (10.1016/j.comptc.2015.06.012_b0070) 1999; 151 Isralewitz (10.1016/j.comptc.2015.06.012_b0110) 2001; 11 Byrd (10.1016/j.comptc.2015.06.012_b0165) 2014; 118 Grimme (10.1016/j.comptc.2015.06.012_b0230) 2010; 132 Watson (10.1016/j.comptc.2015.06.012_b0005) 2014 Malpass (10.1016/j.comptc.2015.06.012_b0175) 2010 Becke (10.1016/j.comptc.2015.06.012_b0220) 1988; 138 Valiev (10.1016/j.comptc.2015.06.012_b0240) 2010; 181 Roy (10.1016/j.comptc.2015.06.012_b0065) 2009; 113 Lu (10.1016/j.comptc.2015.06.012_b0025) 1999; 35 Su (10.1016/j.comptc.2015.06.012_b0105) 2009; 10 Ufimtsev (10.1016/j.comptc.2015.06.012_b0235) 2009; 5 Wolff (10.1016/j.comptc.2015.06.012_b0055) 2011; 84 Binning (10.1016/j.comptc.2015.06.012_b0030) 1986; 56 Ozer (10.1016/j.comptc.2015.06.012_b0135) 2012; 136 Goldstein (10.1016/j.comptc.2015.06.012_b0190) 1980 Ehrenstein (10.1016/j.comptc.2015.06.012_b0050) 2001 Isralewitz (10.1016/j.comptc.2015.06.012_b0020) 2001; 11 Wang (10.1016/j.comptc.2015.06.012_b0090) 2011; 42 Ashkin (10.1016/j.comptc.2015.06.012_b0035) 1987; 235 Onuchic (10.1016/j.comptc.2015.06.012_b0010) 2004; 14 Jarzynski (10.1016/j.comptc.2015.06.012_b0080) 1997; 78 van Gunsteren (10.1016/j.comptc.2015.06.012_b0200) 1982; 45 Germana Paterlini (10.1016/j.comptc.2015.06.012_b0205) 1998; 236 Lee (10.1016/j.comptc.2015.06.012_b0225) 1988; 37 Schmidt (10.1016/j.comptc.2015.06.012_b0245) 1993; 14 Jarzynski (10.1016/j.comptc.2015.06.012_b0085) 1997; 56 Ozer (10.1016/j.comptc.2015.06.012_b0125) 2010; 6 Santamaria (10.1016/j.comptc.2015.06.012_b0180) 2014 Kubo (10.1016/j.comptc.2015.06.012_b0210) 1966; 29-1 Ozer (10.1016/j.comptc.2015.06.012_b0140) 2014; 141 Chandrasekhar (10.1016/j.comptc.2015.06.012_b0215) 1943; 15 Ponmurugan (10.1016/j.comptc.2015.06.012_b0120) 2012; 6 Szilágyi (10.1016/j.comptc.2015.06.012_b0015) 2007 Gutin (10.1016/j.comptc.2015.06.012_b0155) 1998; 108 |
| References_xml | – volume: 11 start-page: 224 year: 2001 end-page: 230 ident: b0110 article-title: Steered molecular dynamics and mechanical functions of proteins publication-title: Curr. Opin. Struct. Biol. – year: 1928 ident: b0195 article-title: The Nature of the Physical World – volume: 29-1 start-page: 255 year: 1966 end-page: 284 ident: b0210 article-title: The fluctuation–dissipation theorem publication-title: Rep. Prog. Phys. – volume: 56 start-page: 930 year: 1986 end-page: 933 ident: b0030 article-title: Atomic force microscope publication-title: Phys. Rev. Lett. – volume: 387 start-page: 308 year: 1997 end-page: 312 ident: b0045 article-title: Elasticity and unfolding of single molecules of the giant protein titin publication-title: Nature – volume: 31 start-page: 699 year: 1998 end-page: 707 ident: b0040 article-title: Laser t-jump induced protein refolding publication-title: Acc., Chem. Res. – volume: 151 start-page: 190 year: 1999 end-page: 211 ident: b0070 article-title: Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations publication-title: J. Comput. Phys. – volume: 45 start-page: 637 year: 1982 end-page: 647 ident: b0200 article-title: Algorithms for Brownian dynamics publication-title: Mol. Phys. – volume: 11 start-page: 224 year: 2001 end-page: 230 ident: b0020 article-title: Steered molecular dynamics and mechanical functions of proteins publication-title: Curr. Opin. Struct. Biol. – volume: 236 start-page: 243 year: 1998 end-page: 252 ident: b0205 article-title: Constant temperature simulations using the Langevin equation with velocity Verlet integration publication-title: Chem. Phys. – volume: 6 start-page: 33 year: 2012 end-page: 45 ident: b0120 article-title: Studies on structural and average unfolding behaviours of FNIII domain of Contactin-1 protein by molecular dynamics simulation publication-title: Front. Life Sci. – reference: D. van der Spoel, E. Lindahl, B. Hess, The GROMACS development team, GROMACS user manual, version 4.6.5, 2013. < – volume: 78 start-page: 2690 year: 1997 end-page: 2693 ident: b0080 article-title: A nonequilibrium equality for free energy differences publication-title: Phys. Rev. Lett. – volume: 14 start-page: 630 year: 2013 end-page: 642 ident: b0170 article-title: Chaperone machines for protein folding, unfolding and disaggregation publication-title: Nat. Rev. Mol. Cell Biol. – volume: 141 start-page: 064101 year: 2014 ident: b0140 article-title: Multiple branched adaptive steered molecular dynamics publication-title: J. Chem. Phys. – year: 2014 ident: b0005 article-title: Molecular biology of the gene – volume: 59 start-page: 6119 year: 1973 end-page: 6127 ident: b0160 article-title: Monte Carlo studies of lattice model polymer chains. III. Relaxation of rouse coordinates publication-title: J. Chem. Phys. – volume: 5 start-page: 2619 year: 2009 end-page: 2628 ident: b0235 article-title: Quantum chemistry on graphical processing units. 3. Analytical energy gradients and first principles molecular dynamics publication-title: J. Chem. Theory Comput. – volume: 9 start-page: 215 year: 1973 end-page: 220 ident: b0185 article-title: Nonlinear generalized Langevin equations publication-title: J. Statist. Phys. – volume: 35 start-page: 453 year: 1999 end-page: 463 ident: b0095 article-title: Steered molecular dynamics simulations of force-induced protein domain unfolding publication-title: Prot.: Struct., Funct., Genet. – volume: 84 start-page: 041934-1 year: 2011 end-page: 041934-7 ident: b0055 article-title: Course-grained model for protein folding based on structural profiles publication-title: Phys. Rev. E – volume: 138 start-page: 3098 year: 1988 end-page: 3100 ident: b0220 article-title: Density-functional exchange-energy approximation with correct asymptotic behavior publication-title: Phys. Rev. A – volume: 10 start-page: 1719 year: 2009 end-page: 1727 ident: b0105 article-title: A molecular dynamics simulation of the human Lysozyme–Camelid VHH HL6 antibody system publication-title: Int. J. Mol. Sci. – volume: 120 start-page: 5946 year: 2004 end-page: 5961 ident: b0075 article-title: Calculating potentials of mean force from steered molecular dynamics simulations publication-title: J. Chem. Phys. – year: 2010 ident: b0175 article-title: Introduction to Industrial Polyethylene: Properties, Catalysts, and Processes – volume: 136 start-page: 215104 year: 2012 ident: b0135 article-title: Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum publication-title: J. Chem. Phys. – reference: Ruben Santamaria, Zwanzig–Langevin molecular dynamics software code, 2014. < – volume: 379 start-page: 494 year: 2008 end-page: 498 ident: b0150 article-title: A steered molecular dynamics method with adaptive direction adjustments publication-title: Bioch. Biophys. Res. Commun. – volume: 118 start-page: 1706 year: 2014 end-page: 1712 ident: b0165 article-title: At what chain length do unbranced alkanes prefer folded conformations? publication-title: J. Phys. ChemPhysChem. A – volume: 132 start-page: 154104 year: 2010 ident: b0230 article-title: A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu publication-title: J. Chem. Phys. – volume: 108 start-page: 6466 year: 1998 end-page: 6483 ident: b0155 article-title: Temperature dependence of the folding rate in a simple protein model: search for a glass transition publication-title: J. Chem. Phys. – volume: 6 start-page: 3026 year: 2010 end-page: 3038 ident: b0125 article-title: Adaptive steered molecular dynamics of the long-distance unfolding of neuropeptide Y publication-title: J. Chem. Theory Comput. – volume: 56 start-page: 5018 year: 1997 end-page: 5035 ident: b0085 article-title: Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach publication-title: Phys. Rev. E – volume: 113 start-page: 7315 year: 2009 end-page: 7321 ident: b0065 article-title: A minima hopping study of all-atom protein folding and structure prediction publication-title: J. Phys. Chem. B – volume: 35 start-page: 453 year: 1999 end-page: 463 ident: b0025 article-title: Steered molecular dynamics simulations of force-induced protein domain unfolding publication-title: Prot.: Struct., Funct., Genet. – volume: 15 start-page: 1 year: 1943 end-page: 89 ident: b0215 article-title: Stochastic problems in physics and astronomy publication-title: Rev. Mod. Phys. – year: 2001 ident: b0050 article-title: Polymeric Materials: Structure, Properties, Applications – volume: 19 start-page: 13 year: 2001 end-page: 25 ident: b0115 article-title: Steered molecular dynamics investigations of protein function publication-title: J. Mol. Graph. Model. – reference: >. – volume: 14 start-page: 70 year: 2004 end-page: 75 ident: b0010 article-title: Theory of protein folding publication-title: Curr. Opin. Struct. Biol. – start-page: 303 year: 2007 end-page: 344, ident: b0015 article-title: Protein folding publication-title: Handbook of Neurochemistry and Molecular Neurobiology – volume: 8 start-page: 4837 year: 2012 end-page: 4844 ident: b0130 article-title: Thermodynamics of decaalanine stretching in water obtained by adaptive steered molecular dynamics simulations publication-title: J. Chem. Theory Comput. – volume: 14 start-page: 1347 year: 1993 end-page: 1363 ident: b0245 article-title: General atomic and molecular electronic structure system publication-title: J. Comput. Chem. – volume: 37 start-page: 785 year: 1988 end-page: 789 ident: b0225 article-title: Development of the Colle–Salvetti correlation energy formula into a functional of the electron density publication-title: Phys. Rev. B – volume: 42 start-page: 719 year: 2011 end-page: 723 ident: b0090 article-title: Free energies and folding mechanics between human prion fragment a-2 domain and b-2 domain under steered molecular dynamics simulations publication-title: J. Taiwan Inst. Chem. Eng. – volume: 70 start-page: 857 year: 2008 end-page: 864 ident: b0145 article-title: A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation publication-title: J. Biochem. Biophys. Meth. – year: 1980 ident: b0190 article-title: Classical Mechanics (Series in Physics) – year: 2014 ident: b0180 article-title: Microscopic pressure cooker model for studying molecules in confinement publication-title: Mol. Phys. – volume: 181 start-page: 1477 year: 2010 end-page: 1489 ident: b0240 article-title: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations publication-title: Comput. Phys. Commun. – volume: 10 start-page: 889 year: 2009 end-page: 905 ident: b0060 article-title: Insights from coarse-grained publication-title: Int. J. Mol. Sci. – volume: 235 start-page: 1517 year: 1987 end-page: 1520 ident: b0035 article-title: Optical trapping and manipulation of viruses and bacteria publication-title: Science – volume: 100 start-page: 2964 year: 2011 end-page: 2973 ident: b0100 article-title: Extension of a three-helix bundle domain of myosin VI and key role of calmodulins publication-title: Biophys. J. – volume: 11 start-page: 224 year: 2001 ident: 10.1016/j.comptc.2015.06.012_b0110 article-title: Steered molecular dynamics and mechanical functions of proteins publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(00)00194-9 – year: 1980 ident: 10.1016/j.comptc.2015.06.012_b0190 – volume: 236 start-page: 243 year: 1998 ident: 10.1016/j.comptc.2015.06.012_b0205 article-title: Constant temperature simulations using the Langevin equation with velocity Verlet integration publication-title: Chem. Phys. doi: 10.1016/S0301-0104(98)00214-6 – ident: 10.1016/j.comptc.2015.06.012_b0255 – volume: 45 start-page: 637 year: 1982 ident: 10.1016/j.comptc.2015.06.012_b0200 article-title: Algorithms for Brownian dynamics publication-title: Mol. Phys. doi: 10.1080/00268978200100491 – volume: 14 start-page: 1347 year: 1993 ident: 10.1016/j.comptc.2015.06.012_b0245 article-title: General atomic and molecular electronic structure system publication-title: J. Comput. Chem. doi: 10.1002/jcc.540141112 – volume: 14 start-page: 70 year: 2004 ident: 10.1016/j.comptc.2015.06.012_b0010 article-title: Theory of protein folding publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/j.sbi.2004.01.009 – volume: 8 start-page: 4837 year: 2012 ident: 10.1016/j.comptc.2015.06.012_b0130 article-title: Thermodynamics of decaalanine stretching in water obtained by adaptive steered molecular dynamics simulations publication-title: J. Chem. Theory Comput. doi: 10.1021/ct300709u – volume: 141 start-page: 064101 year: 2014 ident: 10.1016/j.comptc.2015.06.012_b0140 article-title: Multiple branched adaptive steered molecular dynamics publication-title: J. Chem. Phys. doi: 10.1063/1.4891807 – volume: 108 start-page: 6466 year: 1998 ident: 10.1016/j.comptc.2015.06.012_b0155 article-title: Temperature dependence of the folding rate in a simple protein model: search for a glass transition publication-title: J. Chem. Phys. doi: 10.1063/1.476053 – volume: 70 start-page: 857 year: 2008 ident: 10.1016/j.comptc.2015.06.012_b0145 article-title: A steered molecular dynamics method with direction optimization and its applications on ligand molecule dissociation publication-title: J. Biochem. Biophys. Meth. doi: 10.1016/j.jbbm.2007.10.006 – volume: 6 start-page: 33 year: 2012 ident: 10.1016/j.comptc.2015.06.012_b0120 article-title: Studies on structural and average unfolding behaviours of FNIII domain of Contactin-1 protein by molecular dynamics simulation publication-title: Front. Life Sci. doi: 10.1080/21553769.2013.776995 – volume: 29-1 start-page: 255 year: 1966 ident: 10.1016/j.comptc.2015.06.012_b0210 article-title: The fluctuation–dissipation theorem publication-title: Rep. Prog. Phys. doi: 10.1088/0034-4885/29/1/306 – volume: 37 start-page: 785 year: 1988 ident: 10.1016/j.comptc.2015.06.012_b0225 article-title: Development of the Colle–Salvetti correlation energy formula into a functional of the electron density publication-title: Phys. Rev. B doi: 10.1103/PhysRevB.37.785 – volume: 379 start-page: 494 year: 2008 ident: 10.1016/j.comptc.2015.06.012_b0150 article-title: A steered molecular dynamics method with adaptive direction adjustments publication-title: Bioch. Biophys. Res. Commun. doi: 10.1016/j.bbrc.2008.12.099 – year: 2001 ident: 10.1016/j.comptc.2015.06.012_b0050 – volume: 56 start-page: 5018 year: 1997 ident: 10.1016/j.comptc.2015.06.012_b0085 article-title: Equilibrium free-energy differences from nonequilibrium measurements: a master-equation approach publication-title: Phys. Rev. E doi: 10.1103/PhysRevE.56.5018 – ident: 10.1016/j.comptc.2015.06.012_b0250 – volume: 35 start-page: 453 year: 1999 ident: 10.1016/j.comptc.2015.06.012_b0025 article-title: Steered molecular dynamics simulations of force-induced protein domain unfolding publication-title: Prot.: Struct., Funct., Genet. – volume: 151 start-page: 190 year: 1999 ident: 10.1016/j.comptc.2015.06.012_b0070 article-title: Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations publication-title: J. Comput. Phys. doi: 10.1006/jcph.1999.6218 – volume: 56 start-page: 930 year: 1986 ident: 10.1016/j.comptc.2015.06.012_b0030 article-title: Atomic force microscope publication-title: Phys. Rev. Lett. doi: 10.1103/PhysRevLett.56.930 – volume: 84 start-page: 041934-1 year: 2011 ident: 10.1016/j.comptc.2015.06.012_b0055 article-title: Course-grained model for protein folding based on structural profiles publication-title: Phys. Rev. E doi: 10.1103/PhysRevE.84.041934 – volume: 59 start-page: 6119 year: 1973 ident: 10.1016/j.comptc.2015.06.012_b0160 article-title: Monte Carlo studies of lattice model polymer chains. III. Relaxation of rouse coordinates publication-title: J. Chem. Phys. doi: 10.1063/1.1679979 – volume: 113 start-page: 7315 year: 2009 ident: 10.1016/j.comptc.2015.06.012_b0065 article-title: A minima hopping study of all-atom protein folding and structure prediction publication-title: J. Phys. Chem. B doi: 10.1021/jp8106793 – volume: 78 start-page: 2690 year: 1997 ident: 10.1016/j.comptc.2015.06.012_b0080 article-title: A nonequilibrium equality for free energy differences publication-title: Phys. Rev. Lett. doi: 10.1103/PhysRevLett.78.2690 – year: 2010 ident: 10.1016/j.comptc.2015.06.012_b0175 – year: 2014 ident: 10.1016/j.comptc.2015.06.012_b0005 – volume: 132 start-page: 154104 year: 2010 ident: 10.1016/j.comptc.2015.06.012_b0230 article-title: A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu publication-title: J. Chem. Phys. doi: 10.1063/1.3382344 – volume: 5 start-page: 2619 year: 2009 ident: 10.1016/j.comptc.2015.06.012_b0235 article-title: Quantum chemistry on graphical processing units. 3. Analytical energy gradients and first principles molecular dynamics publication-title: J. Chem. Theory Comput. doi: 10.1021/ct9003004 – volume: 118 start-page: 1706 year: 2014 ident: 10.1016/j.comptc.2015.06.012_b0165 article-title: At what chain length do unbranced alkanes prefer folded conformations? publication-title: J. Phys. ChemPhysChem. A doi: 10.1021/jp4121854 – volume: 9 start-page: 215 year: 1973 ident: 10.1016/j.comptc.2015.06.012_b0185 article-title: Nonlinear generalized Langevin equations publication-title: J. Statist. Phys. doi: 10.1007/BF01008729 – year: 1928 ident: 10.1016/j.comptc.2015.06.012_b0195 – volume: 6 start-page: 3026 year: 2010 ident: 10.1016/j.comptc.2015.06.012_b0125 article-title: Adaptive steered molecular dynamics of the long-distance unfolding of neuropeptide Y publication-title: J. Chem. Theory Comput. doi: 10.1021/ct100320g – volume: 19 start-page: 13 year: 2001 ident: 10.1016/j.comptc.2015.06.012_b0115 article-title: Steered molecular dynamics investigations of protein function publication-title: J. Mol. Graph. Model. doi: 10.1016/S1093-3263(00)00133-9 – volume: 35 start-page: 453 year: 1999 ident: 10.1016/j.comptc.2015.06.012_b0095 article-title: Steered molecular dynamics simulations of force-induced protein domain unfolding publication-title: Prot.: Struct., Funct., Genet. – volume: 15 start-page: 1 year: 1943 ident: 10.1016/j.comptc.2015.06.012_b0215 article-title: Stochastic problems in physics and astronomy publication-title: Rev. Mod. Phys. doi: 10.1103/RevModPhys.15.1 – volume: 120 start-page: 5946 year: 2004 ident: 10.1016/j.comptc.2015.06.012_b0075 article-title: Calculating potentials of mean force from steered molecular dynamics simulations publication-title: J. Chem. Phys. doi: 10.1063/1.1651473 – year: 2014 ident: 10.1016/j.comptc.2015.06.012_b0180 article-title: Microscopic pressure cooker model for studying molecules in confinement publication-title: Mol. Phys. – volume: 181 start-page: 1477 year: 2010 ident: 10.1016/j.comptc.2015.06.012_b0240 article-title: NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations publication-title: Comput. Phys. Commun. doi: 10.1016/j.cpc.2010.04.018 – start-page: 303 year: 2007 ident: 10.1016/j.comptc.2015.06.012_b0015 article-title: Protein folding – volume: 14 start-page: 630 year: 2013 ident: 10.1016/j.comptc.2015.06.012_b0170 article-title: Chaperone machines for protein folding, unfolding and disaggregation publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm3658 – volume: 42 start-page: 719 year: 2011 ident: 10.1016/j.comptc.2015.06.012_b0090 article-title: Free energies and folding mechanics between human prion fragment a-2 domain and b-2 domain under steered molecular dynamics simulations publication-title: J. Taiwan Inst. Chem. Eng. doi: 10.1016/j.jtice.2011.03.003 – volume: 31 start-page: 699 year: 1998 ident: 10.1016/j.comptc.2015.06.012_b0040 article-title: Laser t-jump induced protein refolding publication-title: Acc., Chem. Res. doi: 10.1021/ar970083x – volume: 136 start-page: 215104 year: 2012 ident: 10.1016/j.comptc.2015.06.012_b0135 article-title: Adaptive steered molecular dynamics: validation of the selection criterion and benchmarking energetics in vacuum publication-title: J. Chem. Phys. doi: 10.1063/1.4725183 – volume: 100 start-page: 2964 year: 2011 ident: 10.1016/j.comptc.2015.06.012_b0100 article-title: Extension of a three-helix bundle domain of myosin VI and key role of calmodulins publication-title: Biophys. J. doi: 10.1016/j.bpj.2011.05.010 – volume: 138 start-page: 3098 year: 1988 ident: 10.1016/j.comptc.2015.06.012_b0220 article-title: Density-functional exchange-energy approximation with correct asymptotic behavior publication-title: Phys. Rev. A doi: 10.1103/PhysRevA.38.3098 – volume: 10 start-page: 889 year: 2009 ident: 10.1016/j.comptc.2015.06.012_b0060 article-title: Insights from coarse-grained Go¯ models for protein folding and dynamics publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms10030889 – volume: 387 start-page: 308 year: 1997 ident: 10.1016/j.comptc.2015.06.012_b0045 article-title: Elasticity and unfolding of single molecules of the giant protein titin publication-title: Nature doi: 10.1038/387308a0 – volume: 235 start-page: 1517 year: 1987 ident: 10.1016/j.comptc.2015.06.012_b0035 article-title: Optical trapping and manipulation of viruses and bacteria publication-title: Science doi: 10.1126/science.3547653 – volume: 10 start-page: 1719 year: 2009 ident: 10.1016/j.comptc.2015.06.012_b0105 article-title: A molecular dynamics simulation of the human Lysozyme–Camelid VHH HL6 antibody system publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms10041719 – volume: 11 start-page: 224 year: 2001 ident: 10.1016/j.comptc.2015.06.012_b0020 article-title: Steered molecular dynamics and mechanical functions of proteins publication-title: Curr. Opin. Struct. Biol. doi: 10.1016/S0959-440X(00)00194-9 |
| SSID | ssj0000463012 |
| Score | 2.1071885 |
| Snippet | [Display omitted]
•External potentials in ab-initio calculations can induce the folding of polymers.•A general Langevin equation of motion is deduced with an... |
| SourceID | crossref elsevier |
| SourceType | Enrichment Source Index Database Publisher |
| StartPage | 72 |
| SubjectTerms | Density functional theory External potentials Molecular dynamics Polymer folding |
| Title | Polymer folding via external potentials in ab-initio calculations |
| URI | https://dx.doi.org/10.1016/j.comptc.2015.06.012 |
| Volume | 1068 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3NS8MwFA9jHvQifuL8GDl4jVvSZG2PYzim4hB0sFtJ0hQqsx1bFbz4t_teP4aCKHhsySvlvfTll75ffo-Qy8AJlTgVsECHgkmXeMwEFmUrTRwLbpKwVNu_nw4mM3k7V_MWGTVnYZBWWef-KqeX2bq-06u92Vumae9R4G7F53OANLDQSFT8lNJH_fyrD775z4KKWP2y6InjGRo0J-hKmhcyt0stQ65KIU8ufl6hvqw64z2yW8NFOqzeaJ-0XHZAtkdNl7ZDMnzIF-8vbkWTqoxE31JNG2lnuswLZAPBFKNpRrVhKXKFcgqBsXXfrvURmY2vn0YTVrdFYBbwfcG44zL2Q9tPOHg5MQPupA29QaxgN-cBXIvDWFjjBSbmvvW1sljqw9YFGvANfMLHpJ3lmTsh1PgaIoOqa85KKeFZVnnWE66vNcTOdIjXuCKytWY4tq5YRA057DmqHBihAyPkyHHRIWxjtaw0M_4Y7zdejr7FPoK0_qvl6b8tz8gOXiHzg6tz0i5Wr-4C4EVhuuX86ZKt4c3dZPoJVqHPjw |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3dS8MwEA9zPswX8RPnZx58jVuaZG0fx3BM3YbgBnsLSZpCRdsxq-CLf7u5fgwFUfC17ZVyd7m79H75HUKXgfVEbEVAAhV6hNuYER0YoK3UUeRRHYcF2_5k2hvN-e1CLBpoUJ-FAVhlFfvLmF5E6-pKp9JmZ5kknQcPdis-XbiSxiUazjbQJhfMB9e--qDrHy1AidUtup4gQECiPkJX4LwAul2QGVJRMHlS7-cU9SXtDHfQdlUv4n75SbuoYdM91BrUY9r2Uf8-e3p_tiscl30k_JYoXHM742WWAxzI-RhOUqw0SQAslGFnGVMN7no5QPPh9WwwItVcBGJcgZ8TaimP_NB0Y-rUHOsetdyErBcJt51jrl6LwsgzmgU6or7xlTDQ64PZBcoVOG4NH6JmmqX2CGHtK2caoF2zhnPu3mUEM8yzXaWc8XQbsVoV0lSk4TC74knW6LBHWSpQggIlgOSo10ZkLbUsSTP-eN6vtSy_GV-6uP6r5PG_JS9QazSbjOX4Znp3grbgDsBAqDhFzXz1as9crZHr88KXPgFVQdEl |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Polymer+folding+via+external+potentials+in+ab-initio+calculations&rft.jtitle=Computational+and+theoretical+chemistry&rft.au=Santamaria%2C+Ruben&rft.au=Jones%2C+Keith&rft.au=Arroyo%2C+Maricela&rft.au=Gonz%C3%A1lez-Garc%C3%ADa%2C+Tania&rft.date=2015-09-15&rft.issn=2210-271X&rft.volume=1068&rft.spage=72&rft.epage=80&rft_id=info:doi/10.1016%2Fj.comptc.2015.06.012&rft.externalDBID=n%2Fa&rft.externalDocID=10_1016_j_comptc_2015_06_012 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2210-271X&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2210-271X&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2210-271X&client=summon |