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1.  Dynamics of the Acetylcholinesterase Tetramer 
Biophysical Journal  2007;94(4):1144-1154.
Acetylcholinesterase rapidly hydrolyzes the neurotransmitter acetylcholine in cholinergic synapses, including the neuromuscular junction. The tetramer is the most important functional form of the enzyme. Two low-resolution crystal structures have been solved. One is compact with two of its four peripheral anionic sites (PAS) sterically blocked by complementary subunits. The other is a loose tetramer with all four subunits accessible to solvent. These structures lacked the C-terminal amphipathic t-peptide (WAT domain) that interacts with the proline-rich attachment domain (PRAD). A complete tetramer model (AChEt) was built based on the structure of the PRAD/WAT complex and the compact tetramer. Normal mode analysis suggested that AChEt could exist in several conformations with subunits fluctuating relative to one another. Here, a multiscale simulation involving all-atom molecular dynamics and Cα-based coarse-grained Brownian dynamics simulations was carried out to investigate the large-scale intersubunit dynamics in AChEt. We sampled the ns-μs timescale motions and found that the tetramer indeed constitutes a dynamic assembly of monomers. The intersubunit fluctuation is correlated with the occlusion of the PAS. Such motions of the subunits “gate” ligand-protein association. The gates are open more than 80% of the time on average, which suggests a small reduction in ligand-protein binding. Despite the limitations in the starting model and approximations inherent in coarse graining, these results are consistent with experiments which suggest that binding of a substrate to the PAS is only somewhat hindered by the association of the subunits.
doi:10.1529/biophysj.107.117879
PMCID: PMC2212707  PMID: 17921202
2.  The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides 
Scientific Reports  2013;3:1639.
Solving the crystal structure of Cbl(TKB) in complex with a pentapeptide, pYTPEP, revealed that the PEP region adopted a poly-L-proline type II (PPII) helix. An unnatural amino acid termed a proline-templated glutamic acid (ptE) that constrained both the backbone and sidechain to the bound conformation was synthesized and incorporated into the pYTPXP peptide. We estimated imposing structural constraints onto the backbone and sidechain of the peptide and preorganize it to the bound conformation in solution will yield nearly an order of magnitude improvement in activity. NMR studies confirmed that the ptE-containing peptide adopts the PPII conformation, however, competitive binding studies showed an order of magnitude loss of activity. Given the emphasis that is placed on imposing structural constraints, we provide an example to support the contrary. These results point to conformational flexibility at the interface, which have implications in the design of potent Cbl(TKB)-binding peptides.
doi:10.1038/srep01639
PMCID: PMC3965358  PMID: 23572190
3.  Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics 
BMC Biophysics  2011;4:12.
Background
Phosphopeptide-binding domains mediate many vital cellular processes such as signal transduction and protein recognition. We studied three well-known domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated (FHA) domain. The first two recognize both phosphothreonine (pThr) and phosphoserine (pSer) residues, but FHA has high specificity for pThr residues. Here we used molecular dynamics (MD) simulations to reveal how FHA exclusively chooses pThr and how BRCT and WW recognize both pThr/pSer. The work also investigated the energies and thermodynamic information of intermolecular interactions.
Results
Simulations carried out included wide-type and mutated systems. Through analysis of MD simulations, we found that the conserved His residue defines dual loops feature of the FHA domain, which creates a small cavity reserved for only the methyl group of pThr. These well-organized loop interactions directly response to the pThr binding selectivity, while single loop (the 2nd phosphobinding site of FHA) or in combination with α-helix (BRCT repeats) or β-sheet (WW domain) fail to differentiate pThr/pSer.
Conclusions
Understanding the domain pre-organizations constructed by conserved residues and the driving force of domain-phosphopeptide recognition provides structural insight into pThr specific binding, which also helps in engineering proteins and designing peptide inhibitors.
doi:10.1186/2046-1682-4-12
PMCID: PMC3146460  PMID: 21612598
4.  The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase 
PLoS Computational Biology  2010;6(11):e1000994.
The oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. The synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. The present study used molecular dynamics and Brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (TRPS). TRPS uses a set of α/β–dimeric units to catalyze the last two steps of L-tryptophan biosynthesis, and the rate is remarkably slower in the isolated monomers. Our work shows that without their binding partner, the isolated monomers are stable and more rigid. The substrates can form fairly stable interactions with the protein in both forms when the protein reaches the final ligand–bound conformations. Our simulations also revealed that the α/β–dimeric unit stabilizes the substrate–protein conformation in the ligand binding process, which lowers the conformation transition barrier and helps the protein conformations shift from an open/inactive form to a closed/active form. Brownian dynamics simulations with a coarse-grained model illustrate how protein conformations affect substrate channeling. The results highlight the complex roles of protein oligomerization and the fine balance between rigidity and dynamics in protein function.
Author Summary
Conformational changes of enzymes are often related to regulating and creating an optimal environment for efficient chemistry. An increasing number of evidences also indicate that oligomerization/co-localization of proteins contributes to the efficiency of metabolic pathways. Although static structures have been available for many multi-enzyme complexes, their efficiency is also governed by the synergistic regulation between the multi-units. Our study applies molecular dynamics and Brownian dynamics simulations to the model system, the tryptophan synthase complex. The multi-enzyme complex is a bienzyme nanomachine and its catalytic activity is intimately related to the allosteric signaling and the metabolite transfer between its α– and β–subunits connected by a 25-Å long channel. Our studies suggest that the binding partner is crucial for the ligand binding processes. Although the isolated monomers are stable in the ligand–free state and can form stable interaction if the substrate is in the final bound conformation, it has higher energy barrier when ligand binds to the active site. We also show that the channel does not always exist, but it may be blocked before the enzyme reaches its final bound conformation. The results highlight the importance of forming protein complexes and the cooperative changes during different states.
doi:10.1371/journal.pcbi.1000994
PMCID: PMC2978696  PMID: 21085641
5.  T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles 
T-Analyst is a user-friendly computer program for analyzing trajectories from molecular modeling. Instead of using Cartesian coordinates for protein conformational analysis, T-Analyst is based on internal bond-angle-torsion coordinates in which internal torsion angle movements, such as side-chain rotations, can be easily detected. The program computes entropy and automatically detects and corrects angle periodicity to produce accurate rotameric states of dihedrals. It also clusters multiple conformations and detects dihedral rotations that contribute hinge-like motions. Correlated motions between selected dihedrals can also be observed from the correlation map. T-Analyst focuses on showing changes in protein flexibility between different states and selecting representative protein conformations for molecular docking studies. The program is provided with instructions and full source code in Perl.
doi:10.1007/s10822-010-9376-y
PMCID: PMC2940022  PMID: 20689979
Molecular dynamics; Entropy; Allosteric; Simulation; Drug screening; Docking; HIV protease; AMBER
6.  Diffusional Channeling in the Sulfate-Activating Complex: Combined Continuum Modeling and Coarse-Grained Brownian Dynamics Studies 
Biophysical Journal  2008;95(10):4659-4667.
Enzymes required for sulfur metabolism have been suggested to gain efficiency by restricted diffusion (i.e., channeling) of an intermediate APS2– between active sites. This article describes modeling of the whole channeling process by numerical solution of the Smoluchowski diffusion equation, as well as by coarse-grained Brownian dynamics. The results suggest that electrostatics plays an essential role in the APS2– channeling. Furthermore, with coarse-grained Brownian dynamics, the substrate channeling process has been studied with reactions in multiple active sites. Our simulations provide a bridge for numerical modeling with Brownian dynamics to simulate the complicated reaction and diffusion and raise important questions relating to the electrostatically mediated substrate channeling in vitro, in situ, and in vivo.
doi:10.1529/biophysj.108.140038
PMCID: PMC2576392  PMID: 18689458
7.  The Influence of Macromolecular Crowding on HIV-1 Protease Internal Dynamics 
High macromolecular concentrations, or crowded conditions, have been shown to affect a wide variety of molecular processes, including diffusion, association and dissociation, and protein folding and stability. Here, we model the effect of macromolecular crowding on the internal dynamics of a protein, HIV-1 protease, using Brownian dynamics simulations. HIV-1 protease possesses a pair of flaps which are postulated to open in the early stages of its catalytic mechanism. Compared to low concentrations, close packed concentrations of repulsive crowding agents are found to significantly reduce the fraction of time that the protease is open. Macromolecular crowding is likely to have a major effect on in vivo enzyme activity, and may play an important regulatory role in the viral life cycle.
doi:10.1021/ja060483s
PMCID: PMC2525809  PMID: 16669648

Results 1-7 (7)