Simulation of Spontaneous Substrate Binding Revealing the Binding Pathway and Mechanism and Initial Conformational Response of GlpT

被引:31
作者
Enkavi, Giray
Tajkhorshid, Emad
机构
[1] Univ Illinois, Beckman Inst Adv Sci & Technol, Urbana, IL 61801 USA
[2] Univ Illinois, Coll Med, Dept Biochem, Ctr Biophys & Computat Biol, Urbana, IL 61801 USA
基金
美国国家卫生研究院;
关键词
MAJOR FACILITATOR SUPERFAMILY; COLI GLYCEROL-3-PHOSPHATE TRANSPORTER; ESCHERICHIA-COLI; MOLECULAR-DYNAMICS; VARIABLE STOICHIOMETRY; PHOSPHATE ANTIPORTER; MEMBRANE-TRANSPORT; STRUCTURAL BASIS; ANION-EXCHANGE; PROTEINS;
D O I
10.1021/bi901412a
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Glycerol 3-phosphate transporter (GlpT) mediates the Import of glycerol 3-phosphate (G3P) using the gradient of inorganic phosphate (Pi). To study the process and mechanism of substrate binding and to investigate the protein's initial response, we performed equilibrium simulations of wild-type GlpT and several of its mutant forms in membranes in the presence of all physiologically relevant substrates (P-i(-), P-i(2-), G3P(-), and G3P(2-)). The simulations capture spontaneous Substrate binding of GlpT, driven by the positive electrostatic potential of the lumen. K80 is found to act as a "hook" making the first encounter with the substrate and guiding it toward the binding site, where it binds tightly to R45, a key binding site residue that acts as a "fork" holding the substrate. R269 establishes no direct contact with the substrate during the simulations, a surprising behavior given its structural pseudosymmetry to R45. In all substrate-bound systems, partial closing of the cytoplasmic half of GlpT was observed. The substrate appears to stabilize the partially occluded state, as in the two apo simulations either no closing was observed or the protein reverted to its open form toward the end of the simulation, whereas in all substrate-bound systems, a stable partially closed state was produced. Along with the modulation of the periplasmic salt bridge network, these substrate-induced events destabilize the periplasmic half while inducing a closure in the cytoplasmic half, thus Capturing the early stages of the proposed rocker-switch mechanism in GlpT.
引用
收藏
页码:1105 / 1114
页数:10
相关论文
共 48 条
[1]   Structural comparison of lactose permease and the glycerol-3-phosphate antiporter: members of the major facilitator superfamily [J].
Abramson, J ;
Kaback, HR ;
Iwata, S .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2004, 14 (04) :413-419
[2]   Imaging α-hemolysin with molecular dynamics:: Ionic conductance, osmotic permeability, and the electrostatic potential map [J].
Aksimentiev, A ;
Schulten, K .
BIOPHYSICAL JOURNAL, 2005, 88 (06) :3745-3761
[3]   VARIABLE STOICHIOMETRY OF PHOSPHATE-LINKED ANION-EXCHANGE IN STREPTOCOCCUS-LACTIS - IMPLICATIONS FOR THE MECHANISM OF SUGAR PHOSPHATE-TRANSPORT BY BACTERIA [J].
AMBUDKAR, SV ;
SONNA, LA ;
MALONEY, PC .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1986, 83 (02) :280-284
[4]   High-yield expression and functional analysis of Escherichia coli glycerol-3-phosphate transporter [J].
Auer, M ;
Kim, MJ ;
Lemieux, MJ ;
Villa, A ;
Song, JM ;
Li, XD ;
Wang, DN .
BIOCHEMISTRY, 2001, 40 (22) :6628-6635
[5]   Cloning and characterization of a putative human glycerol 3-phosphate permease gene (SLC37A1 ou G3PP) on 21q22.3: Mutation analysis in two candidate phenotypes, DFNB10 and a glycerol kinase deficiency [J].
Bartoloni, L ;
Wattenhofer, M ;
Kudoh, J ;
Berry, A ;
Shibuya, K ;
Kawasaki, K ;
Wang, J ;
Asakawa, S ;
Talior, I ;
Bonne-Tamir, B ;
Rossier, C ;
Michaud, J ;
McCabe, ERB ;
Minoshima, S ;
Shimizu, N ;
Scott, HS ;
Antonarakis, SE .
GENOMICS, 2000, 70 (02) :190-200
[6]   Helix dynamics in a membrane transport protein: comparative simulations of the glycerol-3-phosphate transporter and its constituent helices [J].
D'rozario, Robert S. G. ;
Sansom, Mark S. P. .
MOLECULAR MEMBRANE BIOLOGY, 2008, 25 (6-7) :571-+
[7]   PARTICLE MESH EWALD - AN N.LOG(N) METHOD FOR EWALD SUMS IN LARGE SYSTEMS [J].
DARDEN, T ;
YORK, D ;
PEDERSEN, L .
JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (12) :10089-10092
[8]   Identification of two essential arginine residues in UhpT, the sugar phosphate antiporter of Escherichia coli [J].
Fann, MC ;
Davies, AH ;
Varadhachary, A ;
Kuroda, T ;
Sevier, C ;
Tsuchiya, T ;
Maloney, PC .
JOURNAL OF MEMBRANE BIOLOGY, 1998, 164 (02) :187-195
[9]   Functional characterization of cysteine residues in GlpT, the glycerol 3-phosphate transporter of Escherichia coli [J].
Fann, MC ;
Busch, A ;
Maloney, PC .
JOURNAL OF BACTERIOLOGY, 2003, 185 (13) :3863-3870
[10]   Functional symmetry of UhpT, the sugar phosphate transporter of Escherichia coli [J].
Fann, MC ;
Maloney, PC .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (50) :33735-33740