Matches in SemOpenAlex for { <https://semopenalex.org/work/W2615697530> ?p ?o ?g. }
Showing items 1 to 74 of
74
with 100 items per page.
- W2615697530 abstract "P1-type ATPases are a special kind of ATP driven pumps which transport soft heavy metals (Cu+, Zn2+, Pb2+ Cd2+) across the cell membranes. Their complete structure is, in general, unknown. We are interested in the structure and dynamics of the transmembrane part of the Cadmium ATPase (CadA) and the metal binding domains of the human Copper transporting Menkes ATPase. Sequence similarity and hydropathy analyses, completed by experiments have shown that soft metal pumps are constituted of 8 transmembrane regions (TMs), compared to 10 for SERCA, the calcium pump for which the 3D structure is known. In collaboration with the biochemists in the laboratory, and using standard programs like MODELLER, CHARMM, XPLOR, AMD together with our own programs, we have predicted the structure of the TMs of CadA. We have built several models of the TM bundle corresponding to several topologies, calculated all atom coordinates with a procedure similar to structure determination from NMR experiments and refined these coordinates using Molecular Dynamics (MD) simulations in an implicit membrane. The Adaptive MD (AMD) program has been used to interactively check the models for bad loop positioning or ''knots'' in the structure. Another interesting feature of P1-type ATPase is the presence of one to six N-terminal conserved GxTCxxC metal binding domain(s) (MBDS). In the case of the Menkes ATPase, there are 6 MBDs, each of them being able to bind Cu$^+$. The structure of each MBD separately is known from NMR spectroscopy but the structure of the assembly is unknown. Using MD simulations, we have studied the dynamics of each MBD in the presence or absence of metal with the final goal of understanding how the metal is transferred from the metallochaperone which binds the metal when it enters the cell to the MBD and why the presence of 6 MBDs is needed for the correct functioning of the pump. These studies have used recent work of researchers in the team on the parameterization of metal ions for molecular mechanics force fields and MD studies on metallochaperones. We show that fast approximate in silico models of metal ions can help understand metal binding and transport in metalloproteins or ATPases, which are known to be major pharmaceutical targets." @default.
- W2615697530 created "2017-05-26" @default.
- W2615697530 creator A5087601874 @default.
- W2615697530 date "2009-11-12" @default.
- W2615697530 modified "2023-09-24" @default.
- W2615697530 title "Structure prediction of P1-type ATPases and molecular dynamics simulations on their Metal Binding Domains" @default.
- W2615697530 cites W2016233481 @default.
- W2615697530 cites W2029667189 @default.
- W2615697530 cites W2074370114 @default.
- W2615697530 cites W2162166182 @default.
- W2615697530 hasPublicationYear "2009" @default.
- W2615697530 type Work @default.
- W2615697530 sameAs 2615697530 @default.
- W2615697530 citedByCount "0" @default.
- W2615697530 crossrefType "dissertation" @default.
- W2615697530 hasAuthorship W2615697530A5087601874 @default.
- W2615697530 hasConcept C118892022 @default.
- W2615697530 hasConcept C139489369 @default.
- W2615697530 hasConcept C147597530 @default.
- W2615697530 hasConcept C170493617 @default.
- W2615697530 hasConcept C181199279 @default.
- W2615697530 hasConcept C185592680 @default.
- W2615697530 hasConcept C23265538 @default.
- W2615697530 hasConcept C24530287 @default.
- W2615697530 hasConcept C2781414619 @default.
- W2615697530 hasConcept C41625074 @default.
- W2615697530 hasConcept C47701112 @default.
- W2615697530 hasConcept C55493867 @default.
- W2615697530 hasConcept C59593255 @default.
- W2615697530 hasConcept C66974803 @default.
- W2615697530 hasConcept C71240020 @default.
- W2615697530 hasConcept C8010536 @default.
- W2615697530 hasConcept C87746105 @default.
- W2615697530 hasConceptScore W2615697530C118892022 @default.
- W2615697530 hasConceptScore W2615697530C139489369 @default.
- W2615697530 hasConceptScore W2615697530C147597530 @default.
- W2615697530 hasConceptScore W2615697530C170493617 @default.
- W2615697530 hasConceptScore W2615697530C181199279 @default.
- W2615697530 hasConceptScore W2615697530C185592680 @default.
- W2615697530 hasConceptScore W2615697530C23265538 @default.
- W2615697530 hasConceptScore W2615697530C24530287 @default.
- W2615697530 hasConceptScore W2615697530C2781414619 @default.
- W2615697530 hasConceptScore W2615697530C41625074 @default.
- W2615697530 hasConceptScore W2615697530C47701112 @default.
- W2615697530 hasConceptScore W2615697530C55493867 @default.
- W2615697530 hasConceptScore W2615697530C59593255 @default.
- W2615697530 hasConceptScore W2615697530C66974803 @default.
- W2615697530 hasConceptScore W2615697530C71240020 @default.
- W2615697530 hasConceptScore W2615697530C8010536 @default.
- W2615697530 hasConceptScore W2615697530C87746105 @default.
- W2615697530 hasLocation W26156975301 @default.
- W2615697530 hasOpenAccess W2615697530 @default.
- W2615697530 hasPrimaryLocation W26156975301 @default.
- W2615697530 hasRelatedWork W1687578534 @default.
- W2615697530 hasRelatedWork W1968993610 @default.
- W2615697530 hasRelatedWork W1991688535 @default.
- W2615697530 hasRelatedWork W2017839008 @default.
- W2615697530 hasRelatedWork W2031626618 @default.
- W2615697530 hasRelatedWork W2044575831 @default.
- W2615697530 hasRelatedWork W2053159064 @default.
- W2615697530 hasRelatedWork W2064065687 @default.
- W2615697530 hasRelatedWork W2064959704 @default.
- W2615697530 hasRelatedWork W2091572397 @default.
- W2615697530 hasRelatedWork W2109731559 @default.
- W2615697530 hasRelatedWork W2142462820 @default.
- W2615697530 hasRelatedWork W2189519565 @default.
- W2615697530 hasRelatedWork W2267921050 @default.
- W2615697530 hasRelatedWork W2325446142 @default.
- W2615697530 hasRelatedWork W2398201425 @default.
- W2615697530 hasRelatedWork W309389463 @default.
- W2615697530 isParatext "false" @default.
- W2615697530 isRetracted "false" @default.
- W2615697530 magId "2615697530" @default.
- W2615697530 workType "dissertation" @default.