FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2894625091> ?p ?o ?g. }

• W2894625091 abstract "ABSTRACT A new version of the coarse-grained (CG) SIRAH force field for proteins has been developed. Modifications to bonded and non-bonded interactions on the existing molecular topologies significantly ameliorate the structural description and flexibility of a non-redundant set of proteins. The SIRAH 2.0 force field has also been ported to the popular simulation package AMBER, which along with the former implementation in GROMACS expands significantly the potential range of users and performance of this CG force field on CPU/GPU codes. As a non-trivial example of application, we undertook the structural and dynamical analysis of the most abundant and conserved calcium-binding protein, namely, Calmodulin (CaM). CaM is constituted by two calcium-binding motifs called EF-hands, which in presence of Calcium specifically recognize a cognate peptide by embracing it. CG simulations of CaM bound to four Calcium ions in the presence or absence of a binding peptide (holo and apo forms, respectively), resulted in good and stable ion coordination. The simulation of the holo form starting from an experimental structure sampled near-native conformations, retrieving quasi-atomistic precision. Removing the binding peptide enabled the EF-hands to perform large reciprocal movements, comparable to those observed in NMR structures. On the other hand, the isolated peptide starting from the helical conformation experienced spontaneous unfolding, in agreement with previous experimental data. However, repositioning the peptide in the neighborhood of one EF-hand not only prevented the peptide unfolding but also drove CaM to a fully bound conformation with both EF-hands embracing the cognate peptide, resembling the experimental holo structure. Therefore, SIRAH 2.0 showed the capacity to handle a number of structurally and dynamically challenging situations including metal ion coordination, unbiased conformational sampling, and specific protein-peptide recognition. TOC." @default.
• W2894625091 created "2018-10-12" @default.
• W2894625091 creator A5002052290 @default.
• W2894625091 creator A5005916377 @default.
• W2894625091 creator A5035123082 @default.
• W2894625091 creator A5069266246 @default.
• W2894625091 creator A5074883529 @default.
• W2894625091 creator A5090684966 @default.
• W2894625091 date "2018-10-05" @default.
• W2894625091 modified "2023-09-23" @default.
• W2894625091 title "The SIRAH force field 2.0: Altius, Fortius, Citius" @default.
• W2894625091 cites W1624860839 @default.
• W2894625091 cites W1892911143 @default.
• W2894625091 cites W1977901028 @default.
• W2894625091 cites W1978498560 @default.
• W2894625091 cites W1978656738 @default.
• W2894625091 cites W1986302333 @default.
• W2894625091 cites W1992898397 @default.
• W2894625091 cites W2001535102 @default.
• W2894625091 cites W2001764614 @default.
• W2894625091 cites W2004822259 @default.
• W2894625091 cites W2019495349 @default.
• W2894625091 cites W2029667189 @default.
• W2894625091 cites W2035266068 @default.
• W2894625091 cites W2035687084 @default.
• W2894625091 cites W2039781258 @default.
• W2894625091 cites W2047261507 @default.
• W2894625091 cites W2050024578 @default.
• W2894625091 cites W2057477511 @default.
• W2894625091 cites W2067174909 @default.
• W2894625091 cites W2081693079 @default.
• W2894625091 cites W2081724315 @default.
• W2894625091 cites W2085611215 @default.
• W2894625091 cites W2123440527 @default.
• W2894625091 cites W2123542377 @default.
• W2894625091 cites W2151319417 @default.
• W2894625091 cites W2165565773 @default.
• W2894625091 cites W2292169708 @default.
• W2894625091 cites W2312727611 @default.
• W2894625091 cites W2313116527 @default.
• W2894625091 cites W2314292783 @default.
• W2894625091 cites W2317735674 @default.
• W2894625091 cites W2319481221 @default.
• W2894625091 cites W2319900881 @default.
• W2894625091 cites W2322376871 @default.
• W2894625091 cites W2322859143 @default.
• W2894625091 cites W2327560429 @default.
• W2894625091 cites W2331280184 @default.
• W2894625091 cites W2334755164 @default.
• W2894625091 cites W2334817875 @default.
• W2894625091 cites W2413334978 @default.
• W2894625091 cites W2416757576 @default.
• W2894625091 cites W2519431390 @default.
• W2894625091 cites W2592827051 @default.
• W2894625091 cites W2742728333 @default.
• W2894625091 cites W2743562142 @default.
• W2894625091 cites W2745974477 @default.
• W2894625091 cites W2751967332 @default.
• W2894625091 cites W2754785233 @default.
• W2894625091 cites W2758013377 @default.
• W2894625091 cites W2758901838 @default.
• W2894625091 cites W2763945826 @default.
• W2894625091 cites W2771490327 @default.
• W2894625091 cites W2794634229 @default.
• W2894625091 cites W2796419182 @default.
• W2894625091 cites W2800668844 @default.
• W2894625091 cites W6850836 @default.
• W2894625091 doi "https://doi.org/10.1101/436774" @default.
• W2894625091 hasPublicationYear "2018" @default.
• W2894625091 type Work @default.
• W2894625091 sameAs 2894625091 @default.
• W2894625091 citedByCount "1" @default.
• W2894625091 countsByYear W28946250912019 @default.
• W2894625091 crossrefType "posted-content" @default.
• W2894625091 hasAuthorship W2894625091A5002052290 @default.
• W2894625091 hasAuthorship W2894625091A5005916377 @default.
• W2894625091 hasAuthorship W2894625091A5035123082 @default.
• W2894625091 hasAuthorship W2894625091A5069266246 @default.
• W2894625091 hasAuthorship W2894625091A5074883529 @default.
• W2894625091 hasAuthorship W2894625091A5090684966 @default.
• W2894625091 hasBestOaLocation W28946250911 @default.
• W2894625091 hasConcept C106251023 @default.
• W2894625091 hasConcept C10803110 @default.
• W2894625091 hasConcept C121332964 @default.
• W2894625091 hasConcept C12554922 @default.
• W2894625091 hasConcept C147597530 @default.
• W2894625091 hasConcept C154945302 @default.
• W2894625091 hasConcept C178790620 @default.
• W2894625091 hasConcept C185592680 @default.
• W2894625091 hasConcept C199360897 @default.
• W2894625091 hasConcept C2777904410 @default.
• W2894625091 hasConcept C2779281246 @default.
• W2894625091 hasConcept C29688787 @default.
• W2894625091 hasConcept C41008148 @default.
• W2894625091 hasConcept C42086223 @default.
• W2894625091 hasConcept C519063684 @default.
• W2894625091 hasConcept C55493867 @default.
• W2894625091 hasConcept C59593255 @default.
• W2894625091 hasConcept C8010536 @default.
• W2894625091 hasConcept C86803240 @default.

• next