1401
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Ishikawa T, Burri RR, Kamatari YO, Sakuraba S, Matubayasi N, Kitao A, Kuwata K. A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method. Phys Chem Chem Phys 2013; 15:3646-54. [DOI: 10.1039/c3cp42761g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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1402
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Troche-Pesqueira E, Pérez-Juste I, Navarro-Vázquez A, Cid MM. A β-cyclodextrin–resveratrol inclusion complex and the role of geometrical and electronic effects on its electronic induced circular dichroism. RSC Adv 2013. [DOI: 10.1039/c3ra41972j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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1403
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Muñoz-García JC, Solera C, Carrero P, de Paz JL, Angulo J, Nieto PM. 3D structure of a heparin mimetic analogue of a FGF-1 activator. A NMR and molecular modelling study. Org Biomol Chem 2013; 11:8269-75. [DOI: 10.1039/c3ob41789a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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1404
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Abstract
Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.
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1405
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Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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1406
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Lamport DTA, Várnai P. Periplasmic arabinogalactan glycoproteins act as a calcium capacitor that regulates plant growth and development. THE NEW PHYTOLOGIST 2013; 197:58-64. [PMID: 23106282 DOI: 10.1111/nph.12005] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/15/2012] [Indexed: 05/18/2023]
Abstract
Arabinogalactan glycoproteins (AGPs) are implicated in virtually all aspects of plant growth and development, yet their precise role remains unknown. Classical AGPs cover the plasma membrane and are highly glycosylated by numerous acidic arabinogalactan polysaccharides O-linked to hydroxyproline. Their heterogeneity and complexity hindered a structural approach until the recent determination of a highly conserved repetitive consensus structure for a 15-sugar residue arabinogalactan subunit with paired glucuronic carboxyls. Based on NMR data and molecular dynamics simulations, we identify these carboxyls as potential intramolecular Ca(2+)-binding sites. Using rapid ultrafiltration assays and mass spectrometry, we verified that AGPs bind Ca(2+) tightly (K(d) ~ 6.5 μM) and stoichiometrically at pH 5. Ca(2+) binding is reversible in a pH-dependent manner. As typical AGPs contain c. 30 Ca(2+)-binding subunits and are bulk components of the periplasm, they represent a Ca(2+) capacitor discharged at low pH by stretch-activated plasma membrane H(+)-ATPases, hence a substantial source of cytosolic Ca(2+). We propose that these Ca(2+) waves prime the 'calcium oscillator', a signal generator essential to the global Ca(2+) signalling pathway of green plants.
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Affiliation(s)
- Derek T A Lamport
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Péter Várnai
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
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1407
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Moradi M, Babin V, Sagui C, Roland C. Recipes for free energy calculations in biomolecular systems. Methods Mol Biol 2013; 924:313-37. [PMID: 23034754 DOI: 10.1007/978-1-62703-017-5_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
During the last decade, several methods for sampling phase space and calculating various free energies in biomolecular systems have been devised or refined for molecular dynamics (MD) simulations. Thus, state-of-the-art methodology and the ever increasing computer power allow calculations that were forbidden a decade ago. These calculations, however, are not trivial as they require knowledge of the methods, insight into the system under study, and, quite often, an artful combination of different methodologies in order to avoid the various traps inherent in an unknown free energy landscape. In this chapter, we illustrate some of these concepts with two relatively simple systems, a sugar ring and proline oligopeptides, whose free energy landscapes still offer considerable challenges. In order to explore the configurational space of these systems, and to surmount the various free energy barriers, we combine three complementary methods: a nonequilibrium umbrella sampling method (adaptively biased MD, or ABMD), replica-exchange molecular dynamics (REMD), and steered molecular dynamics (SMD). In particular, ABMD is used to compute the free energy surface of a set of collective variables; REMD is used to improve the performance of ABMD, to carry out sampling in space complementary to the collective variables, and to sample equilibrium configurations directly; and SMD is used to study different transition mechanisms.
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Affiliation(s)
- Mahmoud Moradi
- Department of Physics, Center for High Performance Simulations, North Carolina State University, Raleigh, NC, USA
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1408
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Jana M, Bandyopadhyay S. Restricted dynamics of water around a protein-carbohydrate complex: computer simulation studies. J Chem Phys 2012; 137:055102. [PMID: 22894384 DOI: 10.1063/1.4739421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Water-mediated protein-carbohydrate interaction is a complex phenomenon responsible for different biological processes in cellular environment. One of the unexplored but important issues in this area is the role played by water during the recognition process and also in controlling the microscopic properties of the complex. In this study, we have carried out atomistic molecular dynamics simulations of a protein-carbohydrate complex formed between the hyaluronan binding domain of the murine Cd44 protein and the octasaccharide hyaluronan in explicit water. Efforts have been made to explore the heterogeneous influence of the complex on the dynamic properties of water present in different regions around it. It is revealed from our analyses that the heterogeneous dynamics of water around the complex are coupled with differential time scales of formation and breaking of hydrogen bonds at the interface. Presence of a highly rigid thin layer of motionally restricted water molecules bridging the protein and the carbohydrate in the common region of the complex has been identified. Such water molecules are expected to play a crucial role in controlling properties of the complex. Importantly, it is demonstrated that the formation of the protein-carbohydrate complex affects the transverse and longitudinal degrees of freedom of the interfacial water molecules in a heterogeneous manner.
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Affiliation(s)
- Madhurima Jana
- Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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1409
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Yamaguchi Y, Nishima W, Re S, Sugita Y. Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2877-2884. [PMID: 23136018 DOI: 10.1002/rcm.6412] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RATIONALE A central issue in glycan mass analysis is the ambiguity of structural assignments due to the heterogeneity and complexity of glycan structures. Ion mobility mass spectrometry (IM-MS) has the potential to separate isomeric glycans depending on their unique collisional cross section especially when coupled with hydrophilic interaction liquid chromatography (HILIC). METHODS Ten pyridylaminated biantennary N-glycans including isomeric structures were measured by electrospray ionization quadrupole-time-of-flight mass spectrometry with an ion mobility phase. We investigated which adduct ions would be suitable for good separation in the ion mobility phase. The differences in observed drift time of isomeric glycans were assessed by molecular dynamics (MD) simulations in vacuum. Connecting an HILIC system with IM-MS provided another, augmented separation mode. RESULTS By selecting doubly protonated precursor ion species, we succeeded in separating a pair of isomeric glycans in the ion mobility phase with reasonable resolution. MD simulations of monogalactosylated glycan isomers indicate that the galactosylated Man α1-3 branch preferentially folds back to the core chitobiose portion to form a compact structure. IM-MS combined with HILIC resulted in even clearer separation of isomeric glycans within 15 min. CONCLUSIONS A combination of IM-MS with an HILIC system is eminently suitable for the confident and rapid distinction of glycan structures within a defined mixture.
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Affiliation(s)
- Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, Chemical Biology Department, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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1410
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Onnainty R, Schenfeld EM, Quevedo MA, Fernández MA, Longhi MR, Granero GE. Characterization of the Hydrochlorothiazide: β-Cyclodextrin Inclusion Complex. Experimental and Theoretical Methods. J Phys Chem B 2012; 117:206-17. [DOI: 10.1021/jp311274c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Renée Onnainty
- Departamento de Farmacia, UNITEFA,
CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, X5000HUA,
Argentina
| | - Esteban M. Schenfeld
- Departamento de Farmacia, UNITEFA,
CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, X5000HUA,
Argentina
| | - Mario A. Quevedo
- Departamento de Farmacia, UNITEFA,
CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, X5000HUA,
Argentina
| | - Mariana A. Fernández
- Departamento
de Química
Orgánica, INFIQC, CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba,
X5000HUA, Argentina
| | - Marcela R. Longhi
- Departamento de Farmacia, UNITEFA,
CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, X5000HUA,
Argentina
| | - Gladys E. Granero
- Departamento de Farmacia, UNITEFA,
CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, X5000HUA,
Argentina
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1411
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Hocking HG, Gerwig GJ, Dutertre S, Violette A, Favreau P, Stöcklin R, Kamerling JP, Boelens R. Structure of the O-glycosylated conopeptide CcTx from Conus consors venom. Chemistry 2012; 19:870-9. [PMID: 23281027 DOI: 10.1002/chem.201202713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Indexed: 01/30/2023]
Abstract
The glycopeptide CcTx, isolated from the venom of the piscivorous cone snail Conus consors, belongs to the κA-family of conopeptides. These toxins elicit excitotoxic responses in the prey by acting on voltage-gated sodium channels. The structure of CcTx, a first in the κA-family, has been determined by high-resolution NMR spectroscopy together with the analysis of its O-glycan at Ser7. A new type of glycopeptide O-glycan core structure, here registered as core type 9, containing two terminal L-galactose units {α-L-Galp-(1→4)-α-D-GlcpNAc-(1→6)-[α-L-Galp-(1→2)-β-D-Galp-(1→3)-]α-D-GalpNAc-(1→O)}, is highlighted. A sequence comparison to other putative members of the κA-family suggests that O-linked glycosylation might be more common than previously thought. This observation alone underlines the requirement for more careful and in-depth investigations into this type of post-translational modification in conotoxins.
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Affiliation(s)
- Henry G Hocking
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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1412
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López CA, de Vries AH, Marrink SJ. Amylose folding under the influence of lipids. Carbohydr Res 2012; 364:1-7. [DOI: 10.1016/j.carres.2012.10.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 11/25/2022]
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1413
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Wehle M, Vilotijevic I, Lipowsky R, Seeberger PH, Varon Silva D, Santer M. Mechanical Compressibility of the Glycosylphosphatidylinositol (GPI) Anchor Backbone Governed by Independent Glycosidic Linkages. J Am Chem Soc 2012; 134:18964-72. [DOI: 10.1021/ja302803r] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marko Wehle
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Ivan Vilotijevic
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Peter H. Seeberger
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
- Department of Chemistry and
Biochemistry, Free University of Berlin, Arnimallee 22, 14195 Berlin, Germany
| | | | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
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1414
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Wang X, Kumar S, Buck PM, Singh SK. Impact of deglycosylation and thermal stress on conformational stability of a full length murine igG2a monoclonal antibody: Observations from molecular dynamics simulations. Proteins 2012; 81:443-60. [DOI: 10.1002/prot.24202] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/04/2012] [Indexed: 12/13/2022]
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1415
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Champion E, Guérin F, Moulis C, Barbe S, Tran TH, Morel S, Descroix K, Monsan P, Mourey L, Mulard LA, Tranier S, Remaud-Siméon M, André I. Applying Pairwise Combinations of Amino Acid Mutations for Sorting Out Highly Efficient Glucosylation Tools for Chemo-Enzymatic Synthesis of Bacterial Oligosaccharides. J Am Chem Soc 2012; 134:18677-88. [DOI: 10.1021/ja306845b] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elise Champion
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Frédéric Guérin
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
- Département de Biologie
Structurale et Biophysique, 205 Route de Narbonne, CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale),
BP 64182, F-31077 Toulouse, France
- Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Claire Moulis
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Sophie Barbe
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Thu Hoai Tran
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
- Département de Biologie
Structurale et Biophysique, 205 Route de Narbonne, CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale),
BP 64182, F-31077 Toulouse, France
- Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Sandrine Morel
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Karine Descroix
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Dr. Roux,
75724 Paris Cedex 15, France
- CNRS UMR3523, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Pierre Monsan
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Lionel Mourey
- Département de Biologie
Structurale et Biophysique, 205 Route de Narbonne, CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale),
BP 64182, F-31077 Toulouse, France
- Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Laurence A. Mulard
- Institut Pasteur, Unité de Chimie des Biomolécules, 28 rue du Dr. Roux,
75724 Paris Cedex 15, France
- CNRS UMR3523, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Samuel Tranier
- Département de Biologie
Structurale et Biophysique, 205 Route de Narbonne, CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale),
BP 64182, F-31077 Toulouse, France
- Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France
| | - Magali Remaud-Siméon
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
| | - Isabelle André
- Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil,
F-31077 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des
Procédés, F-31400 Toulouse, France
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1416
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Badieyan S, Bevan DR, Zhang C. Probing the Active Site Chemistry of β-Glucosidases along the Hydrolysis Reaction Pathway. Biochemistry 2012; 51:8907-18. [DOI: 10.1021/bi300675x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Somayesadat Badieyan
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
| | - David R. Bevan
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
| | - Chenming Zhang
- Department
of Biological Systems Engineering and ‡Department of Biochemistry, Virginia Tech, Blacksburg, Virginia
24061, United States
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1417
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Li L, Chen H, Zhao RN, Han JG. The investigations on HIV-1 gp120 bound with BMS-488043 by using docking and molecular dynamics simulations. J Mol Model 2012; 19:905-17. [PMID: 23086459 DOI: 10.1007/s00894-012-1619-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 09/30/2012] [Indexed: 11/30/2022]
Abstract
BMS-488043, like its predecessor BMS-378806, is a small molecule that can block the interactions between gp120 and CD4, and has shown good clinical efficacy. However, the crystal structure of drug-gp120 complexes or the full-length gp120 free of bound ligand is unpublished until now. Docking combined with molecular dynamics simulation is used to investigate the binding mode between BMS-488043 and gp120. On the basis of the analysis of the simulated results, the plausible binding mode is acquired, such as the changes of binding mode in the trajectory and the calculated binding free energy. Subsequently, a number of residues which make contacts with the small molecule are studied by binding free energy decomposition to understand the mutation experiments, such as Trp427, Ser375, and Thr257 residues with the help of the acquired binding mode above. Especially, the importance of the hydrophobic groove formed by residues Ile371 and Gly472 which bind BMS-488043 is elaborated, which has not been explored much. In addition, theoretical investigations on the dynamics behavior of the gp120 associated with BMS-488043 enhanced binding are performed; the results indicate that the BMS-488043 may be more deeply inserted into the Phe43 cavity compared with the previous binding mode acquired by docking.
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Affiliation(s)
- Liang Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, People's Republic of China
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1418
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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1419
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Stacking interactions between carbohydrate and protein quantified by combination of theoretical and experimental methods. PLoS One 2012; 7:e46032. [PMID: 23056230 PMCID: PMC3466270 DOI: 10.1371/journal.pone.0046032] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 08/28/2012] [Indexed: 11/21/2022] Open
Abstract
Carbohydrate – receptor interactions are an integral part of biological events. They play an important role in many cellular processes, such as cell-cell adhesion, cell differentiation and in-cell signaling. Carbohydrates can interact with a receptor by using several types of intermolecular interactions. One of the most important is the interaction of a carbohydrate's apolar part with aromatic amino acid residues, known as dispersion interaction or CH/π interaction. In the study presented here, we attempted for the first time to quantify how the CH/π interaction contributes to a more general carbohydrate - protein interaction. We used a combined experimental approach, creating single and double point mutants with high level computational methods, and applied both to Ralstonia solanacearum (RSL) lectin complexes with α-l-Me-fucoside. Experimentally measured binding affinities were compared with computed carbohydrate-aromatic amino acid residue interaction energies. Experimental binding affinities for the RSL wild type, phenylalanine and alanine mutants were −8.5, −7.1 and −4.1 kcal.mol−1, respectively. These affinities agree with the computed dispersion interaction energy between carbohydrate and aromatic amino acid residues for RSL wild type and phenylalanine, with values −8.8, −7.9 kcal.mol−1, excluding the alanine mutant where the interaction energy was −0.9 kcal.mol−1. Molecular dynamics simulations show that discrepancy can be caused by creation of a new hydrogen bond between the α-l-Me-fucoside and RSL. Observed results suggest that in this and similar cases the carbohydrate-receptor interaction can be driven mainly by a dispersion interaction.
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1420
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Matsuo K, Namatame H, Taniguchi M, Gekko K. Vacuum-ultraviolet electronic circular dichroism study of methyl α-D-glucopyranoside in aqueous solution by time-dependent density functional theory. J Phys Chem A 2012; 116:9996-10003. [PMID: 22950837 DOI: 10.1021/jp306914s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vacuum-ultraviolet (VUV) electronic circular dichroism (ECD) spectrum of methyl α-D-glucopyranoside (methyl α-D-Glc) was measured down to 163 nm in aqueous solution using a synchrotron-radiation VUV-ECD spectrophotometer. The spectrum exhibited two characteristic ECD peaks around 170 nm, which depend on the trans (T) and gauche (G) configurations of the hydroxymethyl group at C-5. To elucidate the influences of the T and G configurations on the spectrum, the ECD spectra of three rotamers (α-GT, α-GG, and α-TG) of methyl α-D-Glc were calculated using time-dependent density functional theory (TDDFT) combined with molecular dynamics simulation. A linear combination of the ECD spectra of these three rotamers, which differ markedly from each other, produced a methyl α-D-Glc spectrum similar to that observed experimentally. The spectrum was assignable to the n-σ* transitions of the ring oxygen and methoxy oxygen with minor contributions from the hydroxyl oxygen. The differences in α-GT, α-GG, and α-TG spectra were attributed to fluctuations of the configurations of the hydroxymethyl group at C-5 and the hydroxyl group at C-4, which strongly affected the orientations of intramolecular hydrogen bonds around the ring oxygen. These findings demonstrate that combining VUV-ECD and TDDFT is useful for structural characterization of saccharides in aqueous solution.
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Affiliation(s)
- Koichi Matsuo
- Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima 739-0046, Japan.
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1421
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Koyama M, Nishimasu H, Ishitani R, Nureki O. Molecular Dynamics Simulation of Autotaxin: Roles of the Nuclease-like Domain and the Glycan Modification. J Phys Chem B 2012; 116:11798-808. [DOI: 10.1021/jp303198u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michio Koyama
- Department of Biophysics and
Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032,
Japan
| | - Hiroshi Nishimasu
- Department of Biophysics and
Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032,
Japan
| | - Ryuichiro Ishitani
- Department of Biophysics and
Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032,
Japan
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198,
Japan
| | - Osamu Nureki
- Department of Biophysics and
Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032,
Japan
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1422
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Pol-Fachin L, Rusu VH, Verli H, Lins RD. GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates. J Chem Theory Comput 2012; 8:4681-90. [PMID: 26605624 DOI: 10.1021/ct300479h] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An improved parameter set for explicit-solvent simulations of carbohydrates (referred to as GROMOS 53A6GLYC) is presented, allowing proper description of the most stable conformation of all 16 possible aldohexopyranose-based monosaccharides. This set includes refinement of torsional potential parameters associated with the determination of hexopyranose rings conformation by fitting to their corresponding quantum-mechanical profiles. Other parameters, as the rules for third and excluded neighbors, are taken directly from the GROMOS 53A6 force field. Comparisons of the herein presented parameter set to our previous version (GROMOS 45A4), the GLYCAM06 force field, and available NMR data are presented in terms of ring puckering free energies, conformational distribution of the hydroxymethyl group, and glycosidic linkage geometries for 16 selected monosaccharides and eight disaccharides. The proposed parameter modifications have shown a significant improvement for the above-mentioned quantities over the two tested force fields, while retaining full compatibility with the GROMOS 53A6 and 54A7 parameter sets for other classes of biomolecules.
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Affiliation(s)
- Laercio Pol-Fachin
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Victor H Rusu
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
| | - Hugo Verli
- Center of Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.,College of Pharmacy, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Roberto D Lins
- Department of Fundamental Chemistry, Federal University of Pernambuco, Recife, PE, Brazil
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1423
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Wang XY, Ji CG, Zhang JZH. Exploring the Molecular Mechanism of Stabilization of the Adhesion Domains of Human CD2 by N-Glycosylation. J Phys Chem B 2012; 116:11570-7. [DOI: 10.1021/jp304116d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xing Y. Wang
- State Key Laboratory
of Precision
Spectroscopy and Department of Physics, Institute of Theoretical and
Computational Science, East China Normal University, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10012, United
States
| | - Chang G. Ji
- State Key Laboratory
of Precision
Spectroscopy and Department of Physics, Institute of Theoretical and
Computational Science, East China Normal University, Shanghai 200062, China
| | - John Z. H. Zhang
- State Key Laboratory
of Precision
Spectroscopy and Department of Physics, Institute of Theoretical and
Computational Science, East China Normal University, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10012, United
States
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1424
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Manickam Achari V, Nguan HS, Heidelberg T, Bryce RA, Hashim R. Molecular Dynamics Study of Anhydrous Lamellar Structures of Synthetic Glycolipids: Effects of Chain Branching and Disaccharide Headgroup. J Phys Chem B 2012; 116:11626-34. [DOI: 10.1021/jp302292s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Hock Seng Nguan
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
| | | | - Richard A. Bryce
- School of Pharmacy and Pharmaceutical
Sciences, University of Manchester, Manchester,
M13 9PT, U.K
| | - Rauzah Hashim
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
- Kavli Institute
of Theoretical
Physics China, Chinese Academy of Sciences, Beijing 100190, China
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1425
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Abel S, Dupradeau FY, Marchi M. Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water. J Chem Theory Comput 2012; 8:4610-23. [DOI: 10.1021/ct3003207] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stéphane Abel
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
| | - François-Yves Dupradeau
- Laboratoire des glucides, UFR de Pharmacie & CNRS FRE 3517, Université de Picardie-Jules Verne, Amiens, France
| | - Massimo Marchi
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
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1426
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Kirschner KN, Lins RD, Maass A, Soares TA. A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation. J Chem Theory Comput 2012; 8:4719-31. [DOI: 10.1021/ct300534j] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Kirschner
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Bioinformatics, Schloss
Birlinghoven, 53754 Sankt Augustin, Germany
| | - Roberto D. Lins
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
| | - Astrid Maass
- Fraunhofer-Institute for Algorithms
and Scientific Computing (SCAI), Department of Simulation Engineering,
Schloss Birlinghoven, 53754 Sankt Augustin, Germany
| | - Thereza A. Soares
- Department of Fundamental Chemistry,
Federal University of Pernambuco, Cidade Universitária, Recife,
PE 50740-560 Brazil
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1427
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Yongye AB, Calle L, Ardá A, Jiménez-Barbero J, André S, Gabius HJ, Martínez-Mayorga K, Cudic M. Molecular Recognition of the Thomsen-Friedenreich Antigen–Threonine Conjugate by Adhesion/Growth Regulatory Galectin-3: Nuclear Magnetic Resonance Studies and Molecular Dynamics Simulations. Biochemistry 2012; 51:7278-89. [DOI: 10.1021/bi300761s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Austin B. Yongye
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
| | - Luis Calle
- Chemical
and Physical Biology, CIB-CSIC, Madrid,
Spain
| | - Ana Ardá
- Chemical
and Physical Biology, CIB-CSIC, Madrid,
Spain
| | | | - Sabine André
- Institute of Physiological
Chemistry,
Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Joachim Gabius
- Institute of Physiological
Chemistry,
Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Munich, Germany
| | - Karina Martínez-Mayorga
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
| | - Mare Cudic
- Torrey Pines Institute for Molecular Studies, Port Saint Lucie, Florida 34987-2352,
United States
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1428
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Skjevik ÅA, Madej BD, Walker RC, Teigen K. LIPID11: a modular framework for lipid simulations using amber. J Phys Chem B 2012; 116:11124-36. [PMID: 22916730 DOI: 10.1021/jp3059992] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Accurate simulation of complex lipid bilayers has long been a goal in condensed phase molecular dynamics (MD). Structure and function of membrane-bound proteins are highly dependent on the lipid bilayer environment and are challenging to study through experimental methods. Within Amber, there has been limited focus on lipid simulations, although some success has been seen with the use of the General Amber Force Field (GAFF). However, to date there are no dedicated Amber lipid force fields. In this paper we describe a new charge derivation strategy for lipids consistent with the Amber RESP approach and a new atom and residue naming and type convention. In the first instance, we have combined this approach with GAFF parameters. The result is LIPID11, a flexible, modular framework for the simulation of lipids that is fully compatible with the existing Amber force fields. The charge derivation procedure, capping strategy, and nomenclature for LIPID11, along with preliminary simulation results and a discussion of the planned long-term parameter development are presented here. Our findings suggest that LIPID11 is a modular framework feasible for phospholipids and a flexible starting point for the development of a comprehensive, Amber-compatible lipid force field.
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Affiliation(s)
- Åge A Skjevik
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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1429
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Molecular dynamics simulations of carbohydrate-mimetic haptens in complex with a complementary anti-carbohydrate antibody. Carbohydr Res 2012; 358:89-95. [DOI: 10.1016/j.carres.2012.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/22/2012] [Accepted: 05/28/2012] [Indexed: 11/30/2022]
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1430
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Freymann DM, Nakamura Y, Focia PJ, Sakai R, Swanson GT. Structure of a tetrameric galectin from Cinachyrella sp. (ball sponge). ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1163-74. [PMID: 22948917 PMCID: PMC3489101 DOI: 10.1107/s0907444912022834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 05/18/2012] [Indexed: 11/10/2022]
Abstract
The galectins are a family of proteins that bind with highest affinity to N-acetyllactosamine disaccharides, which are common constituents of asparagine-linked complex glycans. They play important and diverse physiological roles, particularly in the immune system, and are thought to be critical metastatic agents for many types of cancer cells, including gliomas. A recent bioactivity-based screen of marine sponge (Cinachyrella sp.) extract identified an ancestral member of the galectin family based on its unexpected ability to positively modulate mammalian ionotropic glutamate receptor function. To gain insight into the mechanistic basis of this activity, the 2.1 Å resolution X-ray structure of one member of the family, galectin CchG-1, is reported. While the protomer exhibited structural similarity to mammalian prototype galectin, CchG-1 adopts a novel tetrameric arrangement in which a rigid toroidal-shaped 'donut' is stabilized in part by the packing of pairs of vicinal disulfide bonds. Twofold symmetry between binding-site pairs provides a basis for a model for interaction with ionotropic glutamate receptors.
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Affiliation(s)
- Douglas M Freymann
- Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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1431
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Re S, Nishima W, Miyashita N, Sugita Y. Conformational flexibility of N-glycans in solution studied by REMD simulations. Biophys Rev 2012; 4:179-187. [PMID: 28510079 DOI: 10.1007/s12551-012-0090-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 06/21/2012] [Indexed: 01/09/2023] Open
Abstract
Protein-glycan recognition regulates a wide range of biological and pathogenic processes. Conformational diversity of glycans in solution is apparently incompatible with specific binding to their receptor proteins. One possibility is that among the different conformational states of a glycan, only one conformer is utilized for specific binding to a protein. However, the labile nature of glycans makes characterizing their conformational states a challenging issue. All-atom molecular dynamics (MD) simulations provide the atomic details of glycan structures in solution, but fairly extensive sampling is required for simulating the transitions between rotameric states. This difficulty limits application of conventional MD simulations to small fragments like di- and tri-saccharides. Replica-exchange molecular dynamics (REMD) simulation, with extensive sampling of structures in solution, provides a valuable way to identify a family of glycan conformers. This article reviews recent REMD simulations of glycans carried out by us or other research groups and provides new insights into the conformational equilibria of N-glycans and their alteration by chemical modification. We also emphasize the importance of statistical averaging over the multiple conformers of glycans for comparing simulation results with experimental observables. The results support the concept of "conformer selection" in protein-glycan recognition.
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Affiliation(s)
- Suyong Re
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Wataru Nishima
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Naoyuki Miyashita
- RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yuji Sugita
- RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN Quantitative Biology Center, IMDA 6F, 1-6-5 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .,RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojimaminamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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1432
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Glass DC, Moritsugu K, Cheng X, Smith JC. REACH Coarse-Grained Simulation of a Cellulose Fiber. Biomacromolecules 2012; 13:2634-44. [DOI: 10.1021/bm300460f] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dennis C. Glass
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Graduate School
of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kei Moritsugu
- Research Program for
Computational Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Xiaolin Cheng
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Department of Biochemistry
and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- UT/ORNL
Center for
Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309,
United States
- Department of Biochemistry
and Molecular and Cellular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
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1433
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Arab-Jaziri F, Bissaro B, Barbe S, Saurel O, Débat H, Dumon C, Gervais V, Milon A, André I, Fauré R, O’Donohue MJ. Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l
-arabinofuranosidase from Thermobacillus xylanilyticus. FEBS J 2012; 279:3598-3611. [DOI: 10.1111/j.1742-4658.2012.08720.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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1434
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Nagata T, Fedorov DG, Sawada T, Kitaura K. Analysis of Solute–Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin–Carbohydrate Complex. J Phys Chem A 2012; 116:9088-99. [DOI: 10.1021/jp304991a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Takeshi Nagata
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29 Yoshidashimo
Adachi, Sakyo-ku, Kyoto 606-8501, Japan
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Toshihiko Sawada
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012,
Japan
| | - Kazuo Kitaura
- Graduate School of Pharmaceutical
Sciences, Kyoto University, 46-29 Yoshidashimo
Adachi, Sakyo-ku, Kyoto 606-8501, Japan
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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1435
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Fuchs PFJ, Hansen HS, Hünenberger PH, Horta BAC. A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol. J Chem Theory Comput 2012; 8:3943-63. [DOI: 10.1021/ct300245h] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick F. J. Fuchs
- INSERM, U665, F-75739 Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France
- Institut National de la Transfusion Sanguine, F-75739 Paris, France
- CNRS, Laboratoire d’Imagerie Paramétrique, UMR 7623, 75006
Paris, France
| | - Halvor S. Hansen
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | | | - Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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1436
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Influenza virus binds its host cell using multiple dynamic interactions. Proc Natl Acad Sci U S A 2012; 109:13626-31. [PMID: 22869709 DOI: 10.1073/pnas.1120265109] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza virus belongs to a wide range of enveloped viruses. The major spike protein hemagglutinin binds sialic acid residues of glycoproteins and glycolipids with dissociation constants in the millimolar range [Sauter NK, et al. (1992) Biochemistry 31:9609-9621], indicating a multivalent binding mode. Here, we characterized the attachment of influenza virus to host cell receptors using three independent approaches. Optical tweezers and atomic force microscopy-based single-molecule force spectroscopy revealed very low interaction forces. Further, the observation of sequential unbinding events strongly suggests a multivalent binding mode between virus and cell membrane. Molecular dynamics simulations reveal a variety of unbinding pathways that indicate a highly dynamic interaction between HA and its receptor, allowing rationalization of influenza virus-cell binding quantitatively at the molecular level.
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1437
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Sameera WMC, Pantazis DA. A Hierarchy of Methods for the Energetically Accurate Modeling of Isomerism in Monosaccharides. J Chem Theory Comput 2012; 8:2630-45. [PMID: 26592108 DOI: 10.1021/ct3002305] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- W. M. C. Sameera
- Institut Català d’Investigació
Química, Av. Països Catalans 16, 43007 Tarragona, Spain
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für
Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim an
der Ruhr, Germany
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1438
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Mishra SK, Sund J, Åqvist J, Koča J. Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. J Comput Chem 2012; 33:2340-50. [DOI: 10.1002/jcc.23081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/25/2012] [Accepted: 07/09/2012] [Indexed: 01/28/2023]
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1439
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Auzanneau FI, Jackson TA, Liao L. Stochastic searches and NMR experiments on four Lewis A analogues: NMR experiments support some flexibility around the fucosidic bond. Bioorg Med Chem 2012; 20:5085-93. [PMID: 22867708 DOI: 10.1016/j.bmc.2012.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/04/2012] [Accepted: 07/10/2012] [Indexed: 11/29/2022]
Abstract
We have compared the conformational behavior of three Le(a) analogues with that of Le(a) using stochastic searches (MOE2005) and selective ROESY experiments. In the analogues either or both the β-d-Gal and α-l-Fuc residues were replaced by β-d-Glc and α-l-Rha units, respectively. All compounds showed similar behavior and even though four conformational families were identified, the calculations and NMR experiments support that the 'stacked conformation' known for Le(a) is predominant for all analogues. Interestingly, ROESY showed a correlation between H-1 Fuc/Rha and H-3 GlcNAc which, although small, could be seen in all analogues. For two compounds, the corresponding distance was measured and found to be shorter (∼3.7Å) than that found in the global minimum (4.5Å). While one published study suggests some motion around the fucosidic bond, this constitutes the first experimental evidence supporting such flexibility. Our MD simulation (Amber10/Glycam06) on Le(a) was in full agreement with previous studies which described a rigid conformation for this branched trisaccharide. Thus, NMR seems to indicate that these dynamic studies are underestimating flexibility around the fucosidic bond.
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1440
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Wilke S, Krausze J, Büssow K. Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx. BMC Biol 2012; 10:62. [PMID: 22809326 PMCID: PMC3409847 DOI: 10.1186/1741-7007-10-62] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/19/2012] [Indexed: 01/09/2023] Open
Abstract
Background The family of lysosome-associated membrane proteins (LAMP) comprises the multifunctional, ubiquitous LAMP-1 and LAMP-2, and the cell type-specific proteins DC-LAMP (LAMP-3), BAD-LAMP (UNC-46, C20orf103) and macrosialin (CD68). LAMPs have been implicated in a multitude of cellular processes, including phagocytosis, autophagy, lipid transport and aging. LAMP-2 isoform A acts as a receptor in chaperone-mediated autophagy. LAMP-2 deficiency causes the fatal Danon disease. The abundant proteins LAMP-1 and LAMP-2 are major constituents of the glycoconjugate coat present on the inside of the lysosomal membrane, the 'lysosomal glycocalyx'. The LAMP family is characterized by a conserved domain of 150 to 200 amino acids with two disulfide bonds. Results The crystal structure of the conserved domain of human DC-LAMP was solved. It is the first high-resolution structure of a heavily glycosylated lysosomal membrane protein. The structure represents a novel β-prism fold formed by two β-sheets bent by β-bulges and connected by a disulfide bond. Flexible loops and a hydrophobic pocket represent possible sites of molecular interaction. Computational models of the glycosylated luminal regions of LAMP-1 and LAMP-2 indicate that the proteins adopt a compact conformation in close proximity to the lysosomal membrane. The models correspond to the thickness of the lysosomal glycoprotein coat of only 5 to 12 nm, according to electron microscopy. Conclusion The conserved luminal domain of lysosome-associated membrane proteins forms a previously unknown β-prism fold. Insights into the structure of the lysosomal glycoprotein coat were obtained by computational models of the LAMP-1 and LAMP-2 luminal regions.
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Affiliation(s)
- Sonja Wilke
- Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstr, 7, 38124 Braunschweig, Germany
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1441
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Zaccheus M, Pendrill R, Jackson TA, Wang A, Auzanneau FI, Widmalm G. Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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1442
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Foley BL, Tessier MB, Woods RJ. Carbohydrate force fields. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2012; 2:652-697. [PMID: 25530813 PMCID: PMC4270206 DOI: 10.1002/wcms.89] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Carbohydrates present a special set of challenges to the generation of force fields. First, the tertiary structures of monosaccharides are complex merely by virtue of their exceptionally high number of chiral centers. In addition, their electronic characteristics lead to molecular geometries and electrostatic landscapes that can be challenging to predict and model. The monosaccharide units can also interconnect in many ways, resulting in a large number of possible oligosaccharides and polysaccharides, both linear and branched. These larger structures contain a number of rotatable bonds, meaning they potentially sample an enormous conformational space. This article briefly reviews the history of carbohydrate force fields, examining and comparing their challenges, forms, philosophies, and development strategies. Then it presents a survey of recent uses of these force fields, noting trends, strengths, deficiencies, and possible directions for future expansion.
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Affiliation(s)
- B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Matthew B. Tessier
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- School of Chemistry, National University of Ireland, Galway, Ireland
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1443
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Islam SM, Roy PN. Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment. J Chem Theory Comput 2012; 8:2412-23. [DOI: 10.1021/ct200789w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Shahidul M. Islam
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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1444
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Zhao Y, Liu X, Wang J, Zhang S. Effects of Cationic Structure on Cellulose Dissolution in Ionic Liquids: A Molecular Dynamics Study. Chemphyschem 2012; 13:3126-33. [DOI: 10.1002/cphc.201200286] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 05/23/2012] [Indexed: 11/08/2022]
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1445
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Lütteke T. The use of glycoinformatics in glycochemistry. Beilstein J Org Chem 2012; 8:915-29. [PMID: 23015842 PMCID: PMC3388882 DOI: 10.3762/bjoc.8.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/29/2012] [Indexed: 01/10/2023] Open
Abstract
Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein-carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed.
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Affiliation(s)
- Thomas Lütteke
- Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany
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1446
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Chen W, Sun S, Li Z. Two glycosylation sites in H5N1 influenza virus hemagglutinin that affect binding preference by computer-based analysis. PLoS One 2012; 7:e38794. [PMID: 22719948 PMCID: PMC3375263 DOI: 10.1371/journal.pone.0038794] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 05/10/2012] [Indexed: 11/25/2022] Open
Abstract
Increasing numbers of H5N1 influenza viruses (IVs) are responsible for human deaths, especially in North Africa and Southeast Asian. The binding of hemagglutinin (HA) on the viral surface to host sialic acid (SA) receptors is a requisite step in the infection process. Phylogenetic analysis reveals that H5N1 viruses can be divided into 10 clades based on their HA sequences, with most human IVs centered from clade 1 and clade 2.1 to clade 2.3. Protein sequence alignment in various clades indicates the high conservation in the receptor-binding domains (RBDs) is essential for binding with the SA receptor. Two glycosylation sites, 158N and 169N, also participate in receptor recognition. In the present work, we attempted to construct a serial H5N1 HA models including diverse glycosylated HAs to simulate the binding process with various SA receptors in silico. As the SA-α-2,3-Gal and SA-α-2,6-Gal receptor adopted two distinctive topologies, straight and fishhook-like, respectively, the presence of N-glycans at 158N would decrease the affinity of HA for all of the receptors, particularly SA-α-2,6-Gal analogs. The steric clashes of the huge glycans shown at another glycosylation site, 169N, located on an adjacent HA monomer, would be more effective in preventing the binding of SA-α-2,3-Gal analogs.
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Affiliation(s)
- Wentian Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, People’s Republic of China
| | - Shisheng Sun
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University, Baltimore, United States of America
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi’an, People’s Republic of China
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1447
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Davies LRL, Pearce OMT, Tessier MB, Assar S, Smutova V, Pajunen M, Sumida M, Sato C, Kitajima K, Finne J, Gagneux P, Pshezhetsky A, Woods R, Varki A. Metabolism of vertebrate amino sugars with N-glycolyl groups: resistance of α2-8-linked N-glycolylneuraminic acid to enzymatic cleavage. J Biol Chem 2012; 287:28917-31. [PMID: 22692207 DOI: 10.1074/jbc.m112.365056] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The sialic acid (Sia) N-acetylneuraminic acid (Neu5Ac) and its hydroxylated derivative N-glycolylneuraminic acid (Neu5Gc) differ by one oxygen atom. CMP-Neu5Gc is synthesized from CMP-Neu5Ac, with Neu5Gc representing a highly variable fraction of total Sias in various tissues and among different species. The exception may be the brain, where Neu5Ac is abundant and Neu5Gc is reported to be rare. Here, we confirm this unusual pattern and its evolutionary conservation in additional samples from various species, concluding that brain Neu5Gc expression has been maintained at extremely low levels over hundreds of millions of years of vertebrate evolution. Most explanations for this pattern do not require maintaining neural Neu5Gc at such low levels. We hypothesized that resistance of α2-8-linked Neu5Gc to vertebrate sialidases is the detrimental effect requiring the relative absence of Neu5Gc from brain. This linkage is prominent in polysialic acid (polySia), a molecule with critical roles in vertebrate neural development. We show that Neu5Gc is incorporated into neural polySia and does not cause in vitro toxicity. Synthetic polymers of Neu5Ac and Neu5Gc showed that mammalian and bacterial sialidases are much less able to hydrolyze α2-8-linked Neu5Gc at the nonreducing terminus. Notably, this difference was not seen with acid-catalyzed hydrolysis of polySias. Molecular dynamics modeling indicates that differences in the three-dimensional conformation of terminal saccharides may partly explain reduced enzymatic activity. In keeping with this, polymers of N-propionylneuraminic acid are sensitive to sialidases. Resistance of Neu5Gc-containing polySia to sialidases provides a potential explanation for the rarity of Neu5Gc in the vertebrate brain.
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Affiliation(s)
- Leela R L Davies
- Department of Medicine, Glycobiology Research and Training Center, University of California San Diego, La Jolla, California 92093-0687, USA
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1448
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Clostridium difficile carbohydrates: glucan in spores, PSII common antigen in cells, immunogenicity of PSII in swine and synthesis of a dual C. difficile–ETEC conjugate vaccine. Carbohydr Res 2012; 354:79-86. [DOI: 10.1016/j.carres.2012.03.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/29/2012] [Accepted: 03/27/2012] [Indexed: 12/11/2022]
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1449
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Zhang Y, Yamamoto S, Yamaguchi T, Kato K. Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide. Molecules 2012; 17:6658-71. [PMID: 22728360 PMCID: PMC6268797 DOI: 10.3390/molecules17066658] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/29/2012] [Accepted: 05/29/2012] [Indexed: 02/05/2023] Open
Abstract
Oligosaccharides of biological importance often exhibit branched covalent structures and dynamic conformational multiplicities. Here we report the application of a method that we developed, which combined molecular dynamics (MD) simulations and lanthanide-assisted paramagnetic NMR spectroscopy, to evaluate the dynamic conformational ensemble of a branched oligosaccharide. A lanthanide-chelating tag was attached to the reducing end of the branched tetrasaccharide of GM2 ganglioside to observe pseudocontact shifts as the source of long distance information for validating the conformational ensemble derived from MD simulations. By inspecting the results, the conformational space of the GM2 tetrasaccharide was compared with that of its nonbranched derivative, the GM3 trisaccharide.
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Affiliation(s)
- Ying Zhang
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Sayoko Yamamoto
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Takumi Yamaguchi
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Koichi Kato
- Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan; (Y.Z.); (S.Y.); (T.Y.)
- Department of Functional Molecular Science, the Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- The Glycoscience Institute, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- GLYENCE Co., Ltd., 2-22-8 Chikusa, Chikusa-ku, Nagoya 464-0858, Japan
- Author to whom correspondence should be addressed; ; Tel.: +81-564-59-5225; Fax: +81-564-59-5224
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1450
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Sattelle BM, Bose-Basu B, Tessier M, Woods RJ, Serianni AS, Almond A. Dependence of pyranose ring puckering on anomeric configuration: methyl idopyranosides. J Phys Chem B 2012; 116:6380-6. [PMID: 22577942 DOI: 10.1021/jp303183y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the aldohexopyranose idose, the unique presence of three axial ring hydroxyl groups causes considerable conformational flexibility, rendering it challenging to study experimentally and an excellent model for rationalizing the relationship between puckering and anomeric configuration. Puckering in methyl α- and β-L-idopyranosides was predicted from kinetically rigorous 10 μs simulations using GLYCAM11 and three explicit water models (TIP3P, TIP4P, and TIP4P-EW). In each case, computed pyranose ring three-bond (vicinal) (1)H-(1)H spin couplings ((3)J(H,H)) trended with NMR measurements. These values, calculated puckering exchange rates and free energies, were independent of the water model. The α- and β-anomers were (1)C(4) chairs for 85 and >99% of their respective trajectories and underwent (1)C(4)→(4)C(1) exchange at rates of 20 μs(-1) and 1 μs(-1). Computed α-anomer (1)C(4)↔(4)C(1) puckering rates depended on the exocyclic C6 substituent, comparing hydroxymethyl with carboxyl from previous work. The slower kinetics and restricted pseudorotational profile of the β-anomer were caused by water occupying a cavity bounded by the anomeric 1-O-methyl and the C6 hydroxymethyl groups. This finding rationalizes the different methyl α- and β-L-idopyranoside (3)J(H,H) values. Identifying a relationship between idopyranose anomeric configuration, microsecond puckering, and water structure facilitates engineering of biologically and commercially important derivatives and underpins deciphering presently elusive structure-function relationships in the glycome.
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Affiliation(s)
- Benedict M Sattelle
- Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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