Halogen–water–hydrogen bridges in biomolecules

Zhou, Peng; Lv, Jing; Zou, Jian‐Wei; Tian, Fengchun; Shang, Zhicai

doi:10.1016/j.jsb.2009.10.006

Cited by 61 publications

(51 citation statements)

References 69 publications

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“…300 The final type of halogen bond observed in protein−ligand crystal structures is that of the halogen−water−hydrogen bridge (XWH). 316 In analogy to the classical HB water bridge, within an XWH bridge one of the HBs is replaced by an XB, but behaves in an otherwise similar way. Computational analysis has indicated that the XWH is thermodynamically stable, and is enhanced by cooperativity between the XB and HB interactions.…”

Section: Analysis Of the Protein Data Bank: Halogen Bonds To Amino Acidsmentioning

confidence: 99%

Halogen Bonding in Supramolecular Chemistry

et al. 2015

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CONTENTS 1. Introduction to Halogen Bonding 7119 1.1. Nature of the Halogen Bond 7119 1.2. Scope of the Review 7120 2. Computational and Theoretical Investigations of Halogen Bonding 7120 2.1.Quantum Mechanics Methods 7120 2.2. σ-Hole Model of Halogen Bonding 7120 2.3. Other Contributions to the Nature of Halogen Bonding 7122 2.4. Recent Examples of Computationally Investigated Halogen-Bonded Complexes 7123 2.4.1. XB to Neutral Species 7123 2.4.2. XB to Anions 7126 2.4.3. XB in Protein−Ligand Complexes 7127 2.4.4. Electron-Transfer Processes Affected by XB Interactions 7127 2.5. Classical Force Field Calculations 7127 2.6. Conclusions and Outlook 7129 3. Gas-Phase Studies of Halogen-Bonding Interactions 7130 4. Halogen Bonding in the Solid State 7131 4.1. Introduction to Crystal Engineering and Functional Materials 7131 4.2. Fundamentals 7132 4.3. Halogen-Bonding Hierarchy 7134 4.3.1. Ranking Halogen-Bond Donors 7134 4.3.2. HB/XB Complementarity/Competition 7136 4.3.3. Predicting XBs 7138 4.4. Control of Solid-State Supramolecular Architectures 7138 4.4.1. Polymorphism 7138 4.4.2. Stoichiometry 7139 4.4.3. Tautomeric Control 7140 4.4.4. XBs Involving Metals and Metal-Bound XBs 7140 4.4.5. XB with Anions in the Solid State 4.5. Solid-State Architectures 4.6.

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Section: Analysis Of the Protein Data Bank: Halogen Bonds To Amino Acidsmentioning

confidence: 99%

Halogen Bonding in Supramolecular Chemistry

et al. 2015

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“…In a previous study, we surveyed all of the high-resolution crystal structures of proteins and of their complexes with small ligands currently deposited in the Protein Data Bank (PDB). We found that 70 protein structures associated with halogenated ligands satisfied the geometric criteria for XWH bridges, giving a total of 84 distinct XWH bridge interactions [10].…”

Section: Introductionmentioning

confidence: 95%

“…Recently, we reported a new mode of interaction for bridging water molecules, namely halogen-water-hydrogen bridges (XWH bridges) [10]. In these bridges the hydrogen bond (H-bond) connecting the ligand and the water molecule is replaced by a halogen bond (X-bond).…”

Section: Introductionmentioning

confidence: 99%

Geometric characteristics and energy landscapes of halogen–water–hydrogen bridges at protein–ligand interfaces

Jiang

Zhou

et al. 2010

Chemical Physics Letters

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“…[7] Subsequently, the optimizations of the predicted enzyme-substrate complexes were performed by using of the QM/MM in the level of AM1:UFF or AM1:AMBER respectively. Finally, the protein-ligand interaction energy (~E int ) in the complex model was calculated according to the strategy proposed by Zhou et al, [26][27][28] this was accomplished by performing single point energy calculation twice, one on the complex system (E1) and other on the same system but its members (enzyme and substrate) were separated by several angstroms of distance each other (E2). in this way the~E int can be derived by E1-E2.…”

Section: Hybrid Qm/mm Analysismentioning

confidence: 99%

“…[32] Recently, one of the most widely applied strategies to implement QM/MM calculations is the ONIOM method, which have been successfully used in studying the nonbonded profile between proteins and ligands. [7][8][26][27][28] In this study, to further refine the binding modes between lipase A mutants and substrate pNPP, the QM/MM approaches were applied to optimize the docked results and predict the binding energies. The results are listed in Table 2.…”

Section: Binding Model Analysismentioning

confidence: 99%

A Combination of Computational and Experimental Approaches to Investigate the Binding Behavior of B.sub Lipase A Mutants with Substrate pNPP

Jin

Zhou

et al. 2011

Molecular Informatics

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The formation of so-called enzyme-substrate complex is the key step for a successful enzyme-catalysis reaction. Enzymes use substrate-binding energy both to promote ground-state association and to stabilize the reaction transition state selectively. Some residues besides the catalytic triads play important roles toward the substrate binding process. In this study, we employed ONIOM methodology and docking to explore the influence of individual amino acids of Bacillus subtilis (B.sub) lipase A on the hydrolysis reaction, with the aim to guide mutagenesis experiments on the basis of computational framework. Subsequently, the B.sub lipase A is modified experimentally with different non-polar residues at the position 12, which is spatially adjacent to the active site, by using site-directed mutagenesis. We obtain a good correlation model between the computationally predicted binding energies and the experimental measured affinities, with a correlation coefficient r=0.78. It is largely unexplored that the combination of docking and quantum mechanical/molecular mechanical (QM/MM) analyses is used in conjunction with experimental procedure to investigate the enzyme catalysis process. We therefore expect that this work could provide a new pathway for exploring the molecular mechanism of enzyme-substrate recognition and interaction.

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Halogen–water–hydrogen bridges in biomolecules

Cited by 61 publications

References 69 publications

Halogen Bonding in Supramolecular Chemistry

Halogen Bonding in Supramolecular Chemistry

Geometric characteristics and energy landscapes of halogen–water–hydrogen bridges at protein–ligand interfaces

A Combination of Computational and Experimental Approaches to Investigate the Binding Behavior of B.sub Lipase A Mutants with Substrate pNPP

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