Glutamine-binding　protein　(GlnBP)　is　one　of　the　periplastic　binding　proteins　from　Gram-negative　bacteria,　whose　crystal　structure　has　been　solved　in　both　open　and　closed　forms.　GlnBP　shares　the　common　architecture　with　the　other　periplastic　binding　proteins　composed　of　two　domains　linked　by　a　hinge　region.　Molecular　dynamics　(MD)　simulations　were　performed　with　the　GROMOS96　program　package　to　study　the　characters　of　GlnBP　in　both　ligand-free　and　ligand-binding　states.　We　also　expected　to　provide　some　useful　hints　for　understanding　the　mechanisms　of　inter-domain　motions　and　ligand　binding　by　analyzing　the　flexibility　of　the　GlnBP.　MD　simulations　reproduced　most　of　the　key　hydrogen　bonds　observed　in　crystal　structure.　Binding　of　the　ligand　induced　the　formation　of　some　stable　hydrogen　bonds,　which　made　the　hinge　strands　more　rigid　and　further　stabilized　the　complex.　The　analysis　of　MD　trajectories　of　2　ns　showed　that　the　open-close　motion　was　coupled　with　inter-domain　twisting　motion　in　the　ligand-free　state,　and　some　loop　regions　in　the　small　domain　contributed　primarily　to　the　flexibility　of　this　protein　while　the　main　secondary　structures　maintained　the　fairly　stable　conformation.　These　motions　seemed　to　shed　some　light　on　the　mechanisms　of　ligand　binding　and　releasing.　All　the　results　kept　in　good　consistence　with　experimental　data.　(c)　2005　Elsevier　B.V.　All　rights　reserved.