Mostra el registre d'ítem simple
A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides
dc.contributor.author | Curcó, David |
dc.contributor.author | Zanuy Gomara, David |
dc.contributor.author | Nussinov, Ruth |
dc.contributor.author | Alemán Llansó, Carlos |
dc.contributor.other | Universitat Politècnica de Catalunya. Departament d'Enginyeria Química |
dc.date.accessioned | 2011-09-14T09:04:48Z |
dc.date.available | 2011-09-14T09:04:48Z |
dc.date.created | 2011-03 |
dc.date.issued | 2011-03 |
dc.identifier.citation | Curcó, D. [et al.]. A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides. "Journal of computational chemistry", Març 2011, vol. 32, núm. 4, p. 607-619. |
dc.identifier.issn | 0192-8651 |
dc.identifier.uri | http://hdl.handle.net/2117/13186 |
dc.description.abstract | A computational strategy to model flexible molecules tethered to a rigid inert surface is presented. The strategy is able to provide uncorrelated relaxed microstructures at the atomistic level. It combines an algorithm to generate molecules tethered to the surface without atomic overlaps, a method to insert solvent molecules and ions in the simulation box, and a powerful relaxation procedure. The reliability of the strategy has been investigated by simulating two different systems: (i) mixed monolayers consisting of binary mixtures of long-chain alkyl thiols of different lengths adsorbed on a rigid inert surface and (ii) CREKA (Cys-Arg-Glu-Lys-Ala), a short linear pentapeptide that recognizes clotted plasma proteins and selectively homes to tumors, covalently tethered to a rigid inert surface in aqueous solution. In the first, we examined the segregation of the two species in the monolayers using different long-chain:short-chain ratios, whereas in the second, we explored the conformational space of CREKA and ions distribution considering densities of peptides per nm2 ranging from 0.03 to 1.67. Results indicate a spontaneous segregation in alkyl thiol monolayers, which enhances when the concentration of longest chains increases. However, the whole conformational profile of CREKA depends on the number of molecules tethered to the surface pointing out the large influence of molecular density on the intermolecular interactions, even though the bioactive conformation was found as the most stable in all cases. |
dc.format.extent | 13 p. |
dc.language.iso | eng |
dc.subject | Àrees temàtiques de la UPC::Enginyeria dels materials |
dc.subject | Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Aplicacions informàtiques a la física i l‘enginyeria |
dc.subject.lcsh | Peptides -- chemistry -- computer simulations |
dc.title | A simulation strategy for the atomistic modeling of flexible molecules covalently tethered to rigid surfaces: application to peptides |
dc.type | Article |
dc.subject.lemac | Pèptids |
dc.contributor.group | Universitat Politècnica de Catalunya. IMEM - Innovació, Modelització i Enginyeria en (BIO) Materials |
dc.identifier.doi | 10.1002/jcc.21647 |
dc.description.peerreviewed | Peer Reviewed |
dc.rights.access | Restricted access - publisher's policy |
local.identifier.drac | 5411735 |
dc.description.version | Postprint (published version) |
local.citation.author | Curcó, D.; Zanuy, D.; Nussinov, R.; Alemán, C. |
local.citation.publicationName | Journal of computational chemistry |
local.citation.volume | 32 |
local.citation.number | 4 |
local.citation.startingPage | 607 |
local.citation.endingPage | 619 |
Fitxers d'aquest items
Aquest ítem apareix a les col·leccions següents
-
Articles de revista [399]
-
Articles de revista [2.227]