J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ bind(1733) structur(1185) ligand(1036) }
{ research(1085) discuss(1038) issu(1018) }
{ structur(1116) can(940) graph(676) }
{ patient(2315) diseas(1263) diabet(1191) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ use(976) code(926) identifi(902) }
{ can(774) often(719) complex(702) }
{ design(1359) user(1324) use(1319) }
{ model(2220) cell(1177) simul(1124) }
{ search(2224) databas(1162) retriev(909) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1119) effect(1106) posit(819) }
{ spatial(1525) area(1432) region(1030) }
{ age(1611) year(1155) adult(843) }
{ group(2977) signific(1463) compar(1072) }
{ first(2504) two(1366) second(1323) }
{ high(1669) rate(1365) level(1280) }
{ survey(1388) particip(1329) question(1065) }
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{ method(1219) similar(1157) match(930) }
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{ health(3367) inform(1360) care(1135) }
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{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ health(1844) social(1437) communiti(874) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Sequence alignment is an important tool for identifying regions of similarities among proteins and for, thus, establishing functional and structural relationships between different proteins. Here, alignments of transmembrane domains (TMDs) of viral channel forming proteins with host ion channels and toxins are evaluated. The following representatives of polytopic viral channel proteins are chosen: (i) p7 of HCV and 2B of Polio virus (two TMDs) and (ii) 3a of SARS-CoV (three TMDs). Using ClustalW2, each of the TMDs of the viral channels is aligned, and the overlap is mapped onto structural models of the host channels and toxins focusing on the pore-lining TMDs. The analysis reveals that p7 and 2B TMDs align with the pore-facing TMD of MscL, and 3a-TMDs align with those of ligand-gated ion channels. Possible implications concerning the mechanism of function of the viral proteins are discussed.

Resumo Limpo

sequenc align import tool identifi region similar among protein thus establish function structur relationship differ protein align transmembran domain tmds viral channel form protein host ion channel toxin evalu follow repres polytop viral channel protein chosen p hcv b polio virus two tmds ii sarscov three tmds use clustalw tmds viral channel align overlap map onto structur model host channel toxin focus porelin tmds analysi reveal p b tmds align porefac tmd mscl atmd align ligandg ion channel possibl implic concern mechan function viral protein discuss

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