ShuT　and　PhuT　are　two　periplasmic　heme　binding　proteins　that　shuttle　heme　between　the　outer　and　inner　membranes　of　the　Gram-negative　bacteria.　Periplasmic　binding　proteins　(PBPs)　generally　exhibit　considerable　conformational　changes　during　the　ligand　binding　process,　whereas　ShuT　and　PhuT　belong　to　a　class　of　PBPs　that　do　not　show　such　behavior　based　on　their　apo　and　holo　crystal　structures.　By　employing　a　series　of　molecular　dynamic　simulations　on　the　ShuT　and　the　PhuT,　the　dynamics　and　functions　of　the　two　PBPs;　were　investigated.　Through　monitoring　the　distance　changes　between　the　two　conserved　glutamates　of　ShuT　and　PhuT,　it　was　found　the　two　PBPs　were　more　flexible　than　previously　assumed,　exhibiting　obvious　opening-closing　motions　which　were　more　remarkable　in　the　apo　runs　of　ShuT.　Based　on　the　results　of　the　domain　motion　analysis,　large　scale　conformational　transitions　were　found　in　all　apo　runs　of　ShuT　and　PhuT,　hinting　that　the　domain　motions　of　the　two　PBPs　may　be　intrinsic.　On　the　basis　of　the　results　of　the　principle　component　analysis,　distinct　opening-closing　and　twisting　motion　tendencies　were　observed　not　only　in　the　apo,　but　also　in　the　holo　simulations　of　the　two　PBPs.　The　Gaussian　network　model　was　applied　in　order　to　analyze　the　hinge　bending　regions.　The　most　important　bending　regions　of　ShuT　and　PhuT　are　located　around　the　midpoints　of　their　respective　connecting　helixes.　Finally,　the　flexibilities　and　the　details　of　the　simulations　of　ShuT　and　PhuT　were　discussed.　Characterized　by　the　remarkably　large　flexibilities,　the　loop　constituted　by　Ala　169,　Gly170　and　Gly171　of　ShuT　and　the　P-turn　constituted　by　Ala176,　Gly177　and　Gly178　of　PhuT　may　be　important　for　the　functions　of　the　two　PBPs.　Furthermore,　the　Asn254　of　ShuT　and　the　Arg228　of　PhuT　may　be　indispensable　for　the　binding　or　unbinding　of　heme,　since　it　is　involved　in　the　important　hydrogen　bonding　to　the　propionate　side-chains　of　heme.　(C)　2008　Elsevier　B.V.　All　rights　reserved.