Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site
Abstract
Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.
- Authors:
-
- Commonwealth Scientific and Industrial Research Organisation, Parkville, VIC (Australia)
- Food and Wine, Univ. of Adelaide, Glen Osmond South Australia (Australia)
- Suranaree Univ. of Technology, Nakhon Ratchasima (Thailand)
- Univ. Grenoble Alpes, Grenoble cedex (France)
- GE Healthcare Life Sciences, Paramatta NSW (Australia)
- Slovak Academy of Sciences, Bratislava (Slovak Republic)
- Centre for Cooperative Research in Biosciences, Derio-Bizkaia (Spain)
- Univ. de Barcelona (Spain)
- Univ. de Barcelona (Spain); Inst. Catalana de Recerca i Estudis Avançats, Barcelona (Spain)
- Univ. Andrés Bello, Talcahuano (Chile); Univ. Autònoma de Barcelona, Bellaterra (Spain)
- Univ. Autònoma de Barcelona, Bellaterra (Spain)
- Univ. Autònoma de Barcelona, Bellaterra (Spain); The Barcelona Inst. of Science and Technology, Tarragona (Spain)
- Univ. of Adelaide, Glen Osmond South Australia (Australia); Huaiyin Normal Univ., Huaian (China)
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- Huaiyin Normal Univ.; Australian Research Council; Suranaree Univ. of Technology; Thailand Research Fund
- OSTI Identifier:
- 1523534
- Grant/Contract Number:
- DP120100900; BRG5980015
- Resource Type:
- Journal Article: Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Computational chemistry; Enzyme mechanisms; Molecular modelling; NMR spectroscopy; X-ray crystallography
Citation Formats
Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, and Hrmova, Maria. Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. United States: N. p., 2019.
Web. doi:10.1038/s41467-019-09691-z.
Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, & Hrmova, Maria. Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. United States. https://doi.org/10.1038/s41467-019-09691-z
Streltsov, Victor A., Luang, Sukanya, Peisley, Alys, Varghese, Joseph N., Ketudat Cairns, James R., Fort, Sebastien, Hijnen, Marcel, Tvaroška, Igor, Ardá, Ana, Jiménez-Barbero, Jesús, Alfonso-Prieto, Mercedes, Rovira, Carme, Mendoza, Fernanda, Tiessler-Sala, Laura, Sánchez-Aparicio, José-Emilio, Rodríguez-Guerra, Jaime, Lluch, José M., Maréchal, Jean-Didier, Masgrau, Laura, and Hrmova, Maria. 2019.
"Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site". United States. https://doi.org/10.1038/s41467-019-09691-z. https://www.osti.gov/servlets/purl/1523534.
@article{osti_1523534,
title = {Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site},
author = {Streltsov, Victor A. and Luang, Sukanya and Peisley, Alys and Varghese, Joseph N. and Ketudat Cairns, James R. and Fort, Sebastien and Hijnen, Marcel and Tvaroška, Igor and Ardá, Ana and Jiménez-Barbero, Jesús and Alfonso-Prieto, Mercedes and Rovira, Carme and Mendoza, Fernanda and Tiessler-Sala, Laura and Sánchez-Aparicio, José-Emilio and Rodríguez-Guerra, Jaime and Lluch, José M. and Maréchal, Jean-Didier and Masgrau, Laura and Hrmova, Maria},
abstractNote = {Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.},
doi = {10.1038/s41467-019-09691-z},
url = {https://www.osti.gov/biblio/1523534},
journal = {Nature Communications},
issn = {2041-1723},
number = 1,
volume = 10,
place = {United States},
year = {Mon May 20 00:00:00 EDT 2019},
month = {Mon May 20 00:00:00 EDT 2019}
}
Web of Science
Works referenced in this record:
Generalized Gradient Approximation Made Simple
journal, October 1996
- Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
- Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase
journal, May 2011
- Hernández-Ortega, Aitor; Borrelli, Kenneth; Ferreira, Patricia
- Biochemical Journal, Vol. 436, Issue 2
Three-dimensional structure of a barley β-D-glucan exohydrolase, a family 3 glycosyl hydrolase
journal, February 1999
- Varghese, Joseph N.; Hrmova, Maria; Fincher, Geoffrey B.
- Structure, Vol. 7, Issue 2
Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
journal, April 1997
- Jones, Gareth; Willett, Peter; Glen, Robert C.
- Journal of Molecular Biology, Vol. 267, Issue 3
Enzyme dynamics point to stepwise conformational selection in catalysis
journal, October 2010
- Ma, Buyong; Nussinov, Ruth
- Current Opinion in Chemical Biology, Vol. 14, Issue 5
GaudiMM: A modular multi-objective platform for molecular modeling
journal, June 2017
- Rodríguez-Guerra Pedregal, Jaime; Sciortino, Giuseppe; Guasp, Jordi
- Journal of Computational Chemistry, Vol. 38, Issue 24
Barley beta-D-Glucan Exohydrolases with beta-D-Glucosidase Activity
journal, March 1996
- Harvey, A. J.
- Journal of Biological Chemistry, Vol. 271, Issue 9
NAMD2: Greater Scalability for Parallel Molecular Dynamics
journal, May 1999
- Kalé, Laxmikant; Skeel, Robert; Bhandarkar, Milind
- Journal of Computational Physics, Vol. 151, Issue 1
Carbohydrate-Binding Proteins: Tertiary Structures and Protein-Sugar Interactions
journal, June 1986
- Quiocho, F. A.
- Annual Review of Biochemistry, Vol. 55, Issue 1
Electrostatic Basis for Enzyme Catalysis
journal, August 2006
- Warshel, Arieh; Sharma, Pankaz K.; Kato, Mitsunori
- Chemical Reviews, Vol. 106, Issue 8
Influence of substrate and product diffusion on the heterogeneous kinetics of enzymic reversible reactions
journal, January 1982
- Marc, Annie; Engasser, Jean Marc
- Journal of Theoretical Biology, Vol. 94, Issue 1
Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles
journal, July 2013
- Fried, S. D.; Boxer, S. G.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
High-resolution crystal structures reveal how a cellulose chain is bound in the 50 Å long tunnel of cellobiohydrolase I from Trichoderma reesei
journal, January 1998
- Divne, Christina; Ståhlberg, Jerry; Teeri, Tuula T.
- Journal of Molecular Biology, Vol. 275, Issue 2, p. 309-325
Thiosugars. I. Synthesis of Derivatives of 2-Amino-2-deoxy-1-thio-D-glucose 1
journal, May 1962
- Horton, D.; Wolfrom, M. L.
- The Journal of Organic Chemistry, Vol. 27, Issue 5
Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
journal, February 2005
- Gutteridge, Alex; Thornton, Janet
- Journal of Molecular Biology, Vol. 346, Issue 1
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977
- Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
- Journal of Computational Physics, Vol. 23, Issue 3
Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides †
journal, July 2001
- Kaminski, George A.; Friesner, Richard A.; Tirado-Rives, Julian
- The Journal of Physical Chemistry B, Vol. 105, Issue 28
Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity
journal, February 2006
- Pieraccini, Stefano; Sironi, Maurizio; Colombo, Giorgio
- Chemical Physics Letters, Vol. 418, Issue 4-6
Crystallisation of Wild-Type and Variant Forms of a Recombinant Plant Enzyme β-D-Glucan Glucohydrolase from Barley (Hordeum vulgare L.) and Preliminary X-ray Analysis
journal, July 2010
- Luang, Sukanya; Cairns, James R. Ketudat; Streltsov, Victor A.
- International Journal of Molecular Sciences, Vol. 11, Issue 7
PROCHECK: a program to check the stereochemical quality of protein structures
journal, April 1993
- Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.
- Journal of Applied Crystallography, Vol. 26, Issue 2
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
New halogenation reagent systems useful for the mild one-step conversion of alcohols into iodides or bromides
journal, December 1988
- Classon, Bjoern; Liu, Zhengchun; Samuelsson, Bertil
- The Journal of Organic Chemistry, Vol. 53, Issue 26
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998
- MacKerell, A. D.; Bashford, D.; Bellott, M.
- The Journal of Physical Chemistry B, Vol. 102, Issue 18
On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR
journal, January 2008
- Díaz, M. Dolores; Fernández-Alonso, María del Carmen; Cuevas, Gabriel
- Pure and Applied Chemistry, Vol. 80, Issue 8
Structure-function relationships of β- D-glucan endo- and exohydrolases from higher plants
journal, September 2001
- Hrmova, Maria; Fincher, Geoffrey B.
- Plant Molecular Biology, Vol. 47, Issue 1/2, p. 73-91
Processivity and substrate-binding in family 18 chitinases
journal, April 2012
- Sørlie, Morten; Zakariassen, Henrik; Norberg, Anne Line
- Biocatalysis and Biotransformation, Vol. 30, Issue 3
Validation of protein models from Cα coordinates alone
journal, October 1997
- Kleywegt, Gerard J.
- Journal of Molecular Biology, Vol. 273, Issue 2
Molecular Recognition of Saccharides by Proteins. Insights on the Origin of the Carbohydrate−Aromatic Interactions
journal, April 2005
- Fernández-Alonso, María del Carmen; Cañada, Francisco Javier; Jiménez-Barbero, Jesús
- Journal of the American Chemical Society, Vol. 127, Issue 20
Development and testing of a general amber force field
journal, January 2004
- Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
- Journal of Computational Chemistry, Vol. 25, Issue 9
Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion
journal, November 2012
- Bacik, John-Paul; Whitworth, Garrett E.; Stubbs, Keith A.
- Chemistry & Biology, Vol. 19, Issue 11
Structural Rationale for Low-Nanomolar Binding of Transition State Mimics to a Family GH3 β- d -Glucan Glucohydrolase from Barley † , ‡
journal, December 2005
- Hrmova, Maria; Streltsov, Victor A.; Smith, Brian J.
- Biochemistry, Vol. 44, Issue 50
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Synthesis of Thio-Linked Disaccharides by 1→2 Intramolecular Thioglycosyl Migration: Oxacarbenium versus Episulfonium Ion Intermediates
journal, July 2000
- Johnston, Blair D.; Pinto, B. Mario
- The Journal of Organic Chemistry, Vol. 65, Issue 15
Dissecting the catalytic mechanism of a plant β-d-glucan glucohydrolase through structural biology using inhibitors and substrate analogues
journal, September 2007
- Hrmova, Maria; Fincher, Geoffrey B.
- Carbohydrate Research, Vol. 342, Issue 12-13
Two-dimensional NMR and All-atom Molecular Dynamics of Cytochrome P450 CYP119 Reveal Hidden Conformational Substates
journal, January 2010
- Lampe, Jed N.; Brandman, Relly; Sivaramakrishnan, Santhosh
- Journal of Biological Chemistry, Vol. 285, Issue 13
Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions
journal, August 2011
- Adamczyk, A. J.; Cao, J.; Kamerlin, S. C. L.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 34
Efficient pseudopotentials for plane-wave calculations
journal, January 1991
- Troullier, N.; Martins, José Luriaas
- Physical Review B, Vol. 43, Issue 3
Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
journal, March 1994
- Varghese, J. N.; Garrett, T. P.; Colman, P. M.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 7
Stereochemistry of polypeptide chain configurations
journal, July 1963
- Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V.
- Journal of Molecular Biology, Vol. 7, Issue 1
GLYCAM06: A generalizable biomolecular force field. Carbohydrates: GLYCAM06
journal, September 2007
- Kirschner, Karl N.; Yongye, Austin B.; Tschampel, Sarah M.
- Journal of Computational Chemistry, Vol. 29, Issue 4
The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
journal, October 2017
- Gygli, Gudrun; Lucas, Maria Fátima; Guallar, Victor
- PLOS Computational Biology, Vol. 13, Issue 10
Barley β-d-glucan exohydrolases. Substrate specificity and kinetic properties
journal, December 1997
- Hrmova, Maria; Fincher, Geoffrey B.
- Carbohydrate Research, Vol. 305, Issue 2
ProDy: Protein Dynamics Inferred from Theory and Experiments
journal, April 2011
- Bakan, A.; Meireles, L. M.; Bahar, I.
- Bioinformatics, Vol. 27, Issue 11, p. 1575-1577
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
journal, August 2004
- Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L.
- Journal of Computational Chemistry, Vol. 25, Issue 11
Processive Catalysis
journal, September 2014
- van Dongen, Stijn F. M.; Elemans, Johannes A. A. W.; Rowan, Alan E.
- Angewandte Chemie International Edition, Vol. 53, Issue 43
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
journal, January 2008
- Barducci, Alessandro; Bussi, Giovanni; Parrinello, Michele
- Physical Review Letters, Vol. 100, Issue 2
Structures and mechanisms of glycosyl hydrolases
journal, September 1995
- Davies, Gideon; Henrissat, Bernard
- Structure, Vol. 3, Issue 9
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
Conformational Diversity in NAD(H) and Interacting Transhydrogenase Nicotinamide Nucleotide Binding Domains
journal, February 2005
- Sundaresan, Vidyasankar; Chartron, Justin; Yamaguchi, Mutsuo
- Journal of Molecular Biology, Vol. 346, Issue 2
PELE web server: atomistic study of biomolecular systems at your fingertips
journal, May 2013
- Madadkar-Sobhani, Armin; Guallar, Victor
- Nucleic Acids Research, Vol. 41, Issue W1
General definition of ring puckering coordinates
journal, March 1975
- Cremer, D.; Pople, J. A.
- Journal of the American Chemical Society, Vol. 97, Issue 6
Coupling between Catalytic Site and Collective Dynamics: A Requirement for Mechanochemical Activity of Enzymes
journal, June 2005
- Yang, Lee-Wei; Bahar, Ivet
- Structure, Vol. 13, Issue 6
Relating Protein Motion to Catalysis
journal, June 2006
- Hammes-Schiffer, Sharon; Benkovic, Stephen J.
- Annual Review of Biochemistry, Vol. 75, Issue 1
Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials
journal, September 2013
- Sørensen, Annette; Lübeck, Mette; Lübeck, Peter
- Biomolecules, Vol. 3, Issue 4
Molecular determinants for selective C 25 -hydroxylation of vitamins D 2 and D 3 by fungal peroxygenases
journal, January 2016
- Lucas, Fátima; Babot, Esteban D.; Cañellas, Marina
- Catalysis Science & Technology, Vol. 6, Issue 1
Three-dimensional Structure of the Barley β-d-Glucan Glucohydrolase in Complex with a Transition State Mimic
journal, November 2003
- Hrmova, Maria; De Gori, Ross; Smith, Brian J.
- Journal of Biological Chemistry, Vol. 279, Issue 6
A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
journal, April 2002
- Laio, Alessandro; VandeVondele, Joost; Rothlisberger, Ursula
- The Journal of Chemical Physics, Vol. 116, Issue 16
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
journal, December 1996
- Mills, J. E. J.; Dean, P. M.
- Journal of Computer-Aided Molecular Design, Vol. 10, Issue 6
XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density
journal, April 1999
- McRee, Duncan E.
- Journal of Structural Biology, Vol. 125, Issue 2-3
Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State
journal, December 2011
- Biarnés, Xevi; Ardèvol, Albert; Iglesias-Fernández, Javier
- Journal of the American Chemical Society, Vol. 133, Issue 50
PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique
journal, November 2005
- Borrelli, Kenneth W.; Vitalis, Andreas; Alcantara, Raul
- Journal of Chemical Theory and Computation, Vol. 1, Issue 6
Canonical dynamics: Equilibrium phase-space distributions
journal, March 1985
- Hoover, William G.
- Physical Review A, Vol. 31, Issue 3
Structural Basis for Broad Substrate Specificity in Higher Plant β-d-Glucan Glucohydrolases
journal, May 2002
- Hrmova, Maria; De Gori, Ross; Smith, Brian J.
- The Plant Cell, Vol. 14, Issue 5
Coupled motions in enzyme catalysis
journal, October 2010
- Nashine, Vishal C.; Hammes-Schiffer, Sharon; Benkovic, Stephen J.
- Current Opinion in Chemical Biology, Vol. 14, Issue 5
Long-timescale simulation methods
journal, April 2005
- Elber, Ron
- Current Opinion in Structural Biology, Vol. 15, Issue 2
Metadynamics: Metadynamics
journal, February 2011
- Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 5
Catalytic Mechanisms and Reaction Intermediates along the Hydrolytic Pathway of a Plant β-D-glucan Glucohydrolase
journal, November 2001
- Hrmova, Maria; Varghese, Joseph N.; De Gori, Ross
- Structure, Vol. 9, Issue 11
Capillary gas chromatography of partially methylated alditol acetates on a high-polarity, cross-linked, fused-silica BPX70 column
journal, May 1993
- Lau, Eva; Bacic, Antony
- Journal of Chromatography A, Vol. 637, Issue 1
Crystal Structures of Paenibacillus polymyxa β-Glucosidase B Complexes Reveal the Molecular Basis of Substrate Specificity and Give New Insights into the Catalytic Machinery of Family I Glycosidases
journal, August 2007
- Isorna, Pablo; Polaina, Julio; Latorre-García, Lorena
- Journal of Molecular Biology, Vol. 371, Issue 5
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
journal, January 1992
- Brünger, Axel T.
- Nature, Vol. 355, Issue 6359
Escaping free-energy minima
journal, September 2002
- Laio, A.; Parrinello, M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling
journal, August 2011
- Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu
- Journal of Chemical Theory and Computation, Vol. 7, Issue 10
Efficient Synthesis of β- d -Mannosides and β- d -Talosides by Double Parallel or Double Serial Inversion
journal, May 2007
- Dong, Hai; Pei, Zhichao; Angelin, Marcus
- The Journal of Organic Chemistry, Vol. 72, Issue 10
High-level expression of barley β-d-glucan exohydrolase HvExoI from a codon-optimized cDNA in Pichia pastoris
journal, September 2010
- Luang, Sukanya; Hrmova, Maria; Ketudat Cairns, James R.
- Protein Expression and Purification, Vol. 73, Issue 1
[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997
- Otwinowski, Zbyszek; Minor, Wladek
- Macromolecular Crystallography Part A, 307-326
Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations
journal, June 2015
- Ardèvol, Albert; Rovira, Carme
- Journal of the American Chemical Society, Vol. 137, Issue 24
Prediction of polymer dissolution in swellable controlled-release systems
journal, December 1987
- Lee, Ping I.; Peppas, Nikolaos A.
- Journal of Controlled Release, Vol. 6, Issue 1
Exploration of Protein Conformational Change with PELE and Meta-Dynamics
journal, February 2012
- Cossins, Benjamin P.; Hosseini, Ali; Guallar, Victor
- Journal of Chemical Theory and Computation, Vol. 8, Issue 3
Electrostatic Basis for Enzyme Catalysis
journal, October 2006
- Warshel, Arieh; Sharma, Pankaz K.; Kato, Mitsunori
- ChemInform, Vol. 37, Issue 42
Mechanism of pore opening in the calcium-activated chloride channel TMEM16A
journal, February 2021
- Lam, Andy K. M.; Dutzler, Raimund
- Nature Communications, Vol. 12, Issue 1
NADPH levels affect cellular epigenetic state by inhibiting HDAC3–Ncor complex
journal, January 2021
- Li, Wei; Kou, Junjie; Qin, Junying
- Nature Metabolism, Vol. 3, Issue 1
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
text, January 2008
- Barducci, Alessandro; Bussi, Giovanni; Parrinello, Michele
- arXiv
Characterization of Ligand Binding by Saturation Transfer Difference NMR Spectroscopy
journal, June 1999
- Mayer, Moriz; Meyer, Bernd
- Angewandte Chemie International Edition, Vol. 38, Issue 12
Development and testing of a general amber force field
journal, January 2004
- Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
- Journal of Computational Chemistry, Vol. 25, Issue 9
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
journal, August 2004
- Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L.
- Journal of Computational Chemistry, Vol. 25, Issue 11
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Metadynamics: Metadynamics
journal, February 2011
- Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 5
A mutant form of mitochondrial GrpE suppresses the sorting defect caused by an alteration in the presequence of Cytochrome b2
journal, October 1997
- Merlin, Alessio; von Ahsen, Oliver; Craig, Elizabeth A.
- Journal of Molecular Biology, Vol. 273, Issue 1
Theory and applications of the transferred nuclear overhauser effect to the study of the conformations of small ligands bound to proteins
journal, July 1982
- Clore, G. M.; Gronenborn, A. M.
- Journal of Magnetic Resonance (1969), Vol. 48, Issue 3
Coupled motions in enzyme catalysis
journal, October 2010
- Nashine, Vishal C.; Hammes-Schiffer, Sharon; Benkovic, Stephen J.
- Current Opinion in Chemical Biology, Vol. 14, Issue 5
Enzyme dynamics point to stepwise conformational selection in catalysis
journal, October 2010
- Ma, Buyong; Nussinov, Ruth
- Current Opinion in Chemical Biology, Vol. 14, Issue 5
Active Site Plasticity within the Glycoside Hydrolase NagZ Underlies a Dynamic Mechanism of Substrate Distortion
journal, November 2012
- Bacik, John-Paul; Whitworth, Garrett E.; Stubbs, Keith A.
- Chemistry & Biology, Vol. 19, Issue 11
Modeling enzymatic processes: A molecular simulation analysis of the origins of regioselectivity
journal, February 2006
- Pieraccini, Stefano; Sironi, Maurizio; Colombo, Giorgio
- Chemical Physics Letters, Vol. 418, Issue 4-6
Conformational Changes Observed in Enzyme Crystal Structures upon Substrate Binding
journal, February 2005
- Gutteridge, Alex; Thornton, Janet
- Journal of Molecular Biology, Vol. 346, Issue 1
Conformational Diversity in NAD(H) and Interacting Transhydrogenase Nicotinamide Nucleotide Binding Domains
journal, February 2005
- Sundaresan, Vidyasankar; Chartron, Justin; Yamaguchi, Mutsuo
- Journal of Molecular Biology, Vol. 346, Issue 2
High-level expression of barley β-d-glucan exohydrolase HvExoI from a codon-optimized cDNA in Pichia pastoris
journal, September 2010
- Luang, Sukanya; Hrmova, Maria; Ketudat Cairns, James R.
- Protein Expression and Purification, Vol. 73, Issue 1
NMR studies of the conformation of thiocellobiose bound to a β-glucosidase from Streptomyces sp
journal, January 1998
- Montero, Esther; Vallmitjana, Miquel; Pérez-Pons, Josep A.
- FEBS Letters, Vol. 421, Issue 3
Electrostatic Basis for Enzyme Catalysis
journal, August 2006
- Warshel, Arieh; Sharma, Pankaz K.; Kato, Mitsunori
- Chemical Reviews, Vol. 106, Issue 8
PELE: Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique
journal, November 2005
- Borrelli, Kenneth W.; Vitalis, Andreas; Alcantara, Raul
- Journal of Chemical Theory and Computation, Vol. 1, Issue 6
Exploration of Protein Conformational Change with PELE and Meta-Dynamics
journal, February 2012
- Cossins, Benjamin P.; Hosseini, Ali; Guallar, Victor
- Journal of Chemical Theory and Computation, Vol. 8, Issue 3
Molecular Recognition of Saccharides by Proteins. Insights on the Origin of the Carbohydrate−Aromatic Interactions
journal, April 2005
- Fernández-Alonso, María del Carmen; Cañada, Francisco Javier; Jiménez-Barbero, Jesús
- Journal of the American Chemical Society, Vol. 127, Issue 20
Catalytic Itinerary in 1,3-1,4-β-Glucanase Unraveled by QM/MM Metadynamics. Charge Is Not Yet Fully Developed at the Oxocarbenium Ion-like Transition State
journal, December 2011
- Biarnés, Xevi; Ardèvol, Albert; Iglesias-Fernández, Javier
- Journal of the American Chemical Society, Vol. 133, Issue 50
Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from ab Initio Quantum Mechanics/Molecular Mechanics Dynamic Simulations
journal, June 2015
- Ardèvol, Albert; Rovira, Carme
- Journal of the American Chemical Society, Vol. 137, Issue 24
Synthesis of Thio-Linked Disaccharides by 1→2 Intramolecular Thioglycosyl Migration: Oxacarbenium versus Episulfonium Ion Intermediates
journal, July 2000
- Johnston, Blair D.; Pinto, B. Mario
- The Journal of Organic Chemistry, Vol. 65, Issue 15
Conversion of 2-Amino-2-deoxy-1-thio-D-glucose Derivatives into Glycosyl Halide Derivatives. A Tetra-O-acetylglycosylsulfenyl Bromide1
journal, November 1963
- Horton, D.; Wolfrom, M. L.; Garg, H. G.
- The Journal of Organic Chemistry, Vol. 28, Issue 11
Thiosugars. I. Synthesis of Derivatives of 2-Amino-2-deoxy-1-thio-D-glucose 1
journal, May 1962
- Horton, D.; Wolfrom, M. L.
- The Journal of Organic Chemistry, Vol. 27, Issue 5
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998
- MacKerell, A. D.; Bashford, D.; Bellott, M.
- The Journal of Physical Chemistry B, Vol. 102, Issue 18
Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus
journal, September 2010
- Yoshida, Erina; Hidaka, Masafumi; Fushinobu, Shinya
- Biochemical Journal, Vol. 431, Issue 1
Crystal structures of glycoside hydrolase family 3 β-glucosidase 1 from Aspergillus aculeatus
journal, May 2013
- Suzuki, Kentaro; Sumitani, Jun-Ichi; Nam, Young-Woo
- Biochemical Journal, Vol. 452, Issue 2
A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
journal, April 2002
- Laio, Alessandro; VandeVondele, Joost; Rothlisberger, Ursula
- The Journal of Chemical Physics, Vol. 116, Issue 16
“Eppur si muove” (yet it moves)
journal, September 2011
- Moliner, Vicent
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 37
Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles
journal, July 2013
- Fried, S. D.; Boxer, S. G.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 30
Escaping free-energy minima
journal, September 2002
- Laio, A.; Parrinello, M.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis
journal, April 2013
- McAndrew, Ryan P.; Park, Joshua I.; Heins, Richard A.
- Journal of Biological Chemistry, Vol. 288, Issue 21
Mutated Barley (1,3)-β-d
-Glucan Endohydrolases Synthesize Crystalline (1,3)-β-d
-Glucans
journal, May 2002
- Hrmova, Maria; Imai, Tomoya; Rutten, Simon J.
- Journal of Biological Chemistry, Vol. 277, Issue 33
ProDy: Protein Dynamics Inferred from Theory and Experiments
journal, April 2011
- Bakan, A.; Meireles, L. M.; Bahar, I.
- Bioinformatics, Vol. 27, Issue 11, p. 1575-1577
The carbohydrate-active enzymes database (CAZy) in 2013
journal, November 2013
- Lombard, Vincent; Golaconda Ramulu, Hemalatha; Drula, Elodie
- Nucleic Acids Research, Vol. 42, Issue D1
PELE web server: atomistic study of biomolecular systems at your fingertips
journal, May 2013
- Madadkar-Sobhani, Armin; Guallar, Victor
- Nucleic Acids Research, Vol. 41, Issue W1
Foolish Seedlings and DELLA Regulators
journal, January 2002
- Eckardt, Nancy A.
- The Plant Cell, Vol. 14, Issue 1
Crystal structure of native α-L -rhamnosidase from Aspergillus terreus
journal, October 2018
- Pachl, Petr; Škerlová, Jana; Šimčíková, Daniela
- Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 11
Carbohydrate-Binding Proteins: Tertiary Structures and Protein-Sugar Interactions
journal, June 1986
- Quiocho, F. A.
- Annual Review of Biochemistry, Vol. 55, Issue 1
Relating Protein Motion to Catalysis
journal, June 2006
- Hammes-Schiffer, Sharon; Benkovic, Stephen J.
- Annual Review of Biochemistry, Vol. 75, Issue 1
The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths
journal, October 2017
- Gygli, Gudrun; Lucas, Maria Fátima; Guallar, Victor
- PLOS Computational Biology, Vol. 13, Issue 10
Processivity and substrate-binding in family 18 chitinases
journal, April 2012
- Sørlie, Morten; Zakariassen, Henrik; Norberg, Anne Line
- Biocatalysis and Biotransformation, Vol. 30, Issue 3
Crystallisation of Wild-Type and Variant Forms of a Recombinant Plant Enzyme β-D-Glucan Glucohydrolase from Barley (Hordeum vulgare L.) and Preliminary X-ray Analysis
journal, July 2010
- Luang, Sukanya; Cairns, James R. Ketudat; Streltsov, Victor A.
- International Journal of Molecular Sciences, Vol. 11, Issue 7
Works referencing / citing this record:
GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
journal, June 2019
- Sánchez-Aparicio, José-Emilio; Sciortino, Giuseppe; Herrmannsdoerfer, Daniel Viladrich
- International Journal of Molecular Sciences, Vol. 20, Issue 13
GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm
journal, June 2019
- Sánchez-Aparicio, José-Emilio; Sciortino, Giuseppe; Herrmannsdoerfer, Daniel Viladrich
- International Journal of Molecular Sciences, Vol. 20, Issue 13