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Fontana C, de Meirelles JL, Verli H. Theoretical models of staurosporine and analogs uncover detailed structural information in biological solution. J Mol Graph Model 2024; 126:108653. [PMID: 37922640 DOI: 10.1016/j.jmgm.2023.108653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.
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Affiliation(s)
- Crisciele Fontana
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - João Luiz de Meirelles
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil
| | - Hugo Verli
- Universidade Federal do Rio Grande do Sul, Centro de Biotecnologia, Av. Bento Gonçalves, 9500 (Caixa Postal 15005), Porto Alegre, CEP 91501-970, RS, Brazil.
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2
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de Meirelles JL, Nepomuceno FC, Peña-García J, Schmidt RR, Pérez-Sánchez H, Verli H. Current Status of Carbohydrates Information in the Protein Data Bank. J Chem Inf Model 2020; 60:684-699. [PMID: 31961683 DOI: 10.1021/acs.jcim.9b00874] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Carbohydrates are well known for their physicochemical, biological, functional, and therapeutic characteristics. Unfortunately, their chemical nature imposes severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available in the Protein Data Bank (PDB). From high quality structures, it is clear that most of the data are highly concentrated on a few sets of residue types, on their monosaccharidic forms, and connected by a small diversity of glycosidic linkages. The geometries of these linkages can be mostly associated with the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified, and located in a pseudorotational equilibrium landscape, not only to local minima but also to transitional states. These qualitative and quantitative analyses offer a global picture of the carbohydrate structural content in the PDB, potentially supporting the building of new models for carbohydrate-related biological phenomena at the atomistic level, including new developments on force field parameters.
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Affiliation(s)
- João L de Meirelles
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
| | - Felipe C Nepomuceno
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
| | - Jorge Peña-García
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Ricardo Rodríguez Schmidt
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department , Universidad Católica de Murcia (UCAM) , Murcia , Spain 30107
| | - Hugo Verli
- Programa de Pos-Graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia , Universidade Federal do Rio Grande do Sul (UFRGS) , Av. Bento Goncalves, 9500 , Porto Alegre , Brazil 91509-900
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3
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Solís D, Bovin NV, Davis AP, Jiménez-Barbero J, Romero A, Roy R, Smetana K, Gabius HJ. A guide into glycosciences: How chemistry, biochemistry and biology cooperate to crack the sugar code. Biochim Biophys Acta Gen Subj 2014; 1850:186-235. [PMID: 24685397 DOI: 10.1016/j.bbagen.2014.03.016] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/17/2023]
Abstract
BACKGROUND The most demanding challenge in research on molecular aspects within the flow of biological information is posed by the complex carbohydrates (glycan part of cellular glycoconjugates). How the 'message' encoded in carbohydrate 'letters' is 'read' and 'translated' can only be unraveled by interdisciplinary efforts. SCOPE OF REVIEW This review provides a didactic step-by-step survey of the concept of the sugar code and the way strategic combination of experimental approaches characterizes structure-function relationships, with resources for teaching. MAJOR CONCLUSIONS The unsurpassed coding capacity of glycans is an ideal platform for generating a broad range of molecular 'messages'. Structural and functional analyses of complex carbohydrates have been made possible by advances in chemical synthesis, rendering production of oligosaccharides, glycoclusters and neoglycoconjugates possible. This availability facilitates to test the glycans as ligands for natural sugar receptors (lectins). Their interaction is a means to turn sugar-encoded information into cellular effects. Glycan/lectin structures and their spatial modes of presentation underlie the exquisite specificity of the endogenous lectins in counterreceptor selection, that is, to home in on certain cellular glycoproteins or glycolipids. GENERAL SIGNIFICANCE Understanding how sugar-encoded 'messages' are 'read' and 'translated' by lectins provides insights into fundamental mechanisms of life, with potential for medical applications.
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Affiliation(s)
- Dolores Solís
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, 28006 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), 07110 Bunyola, Mallorca, Illes Baleares, Spain.
| | - Nicolai V Bovin
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul Miklukho-Maklaya 16/10, 117871 GSP-7, V-437, Moscow, Russian Federation.
| | - Anthony P Davis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Jesús Jiménez-Barbero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - Antonio Romero
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9, 28040 Madrid, Spain.
| | - René Roy
- Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
| | - Karel Smetana
- Charles University, 1st Faculty of Medicine, Institute of Anatomy, U nemocnice 3, 128 00 Prague 2, Czech Republic.
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany.
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Examination of the influence of C5-hydroxymethyl group and configurations of hydroxyl groups at C2, C3, and C4 stereocentres on the N-glycosidic torsion: synthesis and X-ray crystallographic investigation of N-(d-ribopyranosyl)alkanamides as N-glycoprotein linkage region analogs. Carbohydr Res 2014; 384:37-45. [DOI: 10.1016/j.carres.2013.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/03/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022]
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Srivastava A, Varghese B, Loganathan D. Exploring the Effect of Bioisosteric Replacement of Carboxamide by a Sulfonamide Moiety on N-Glycosidic Torsions and Molecular Assembly: Synthesis and X-ray Crystallographic Investigation of N-(β-D-Glycosyl)sulfonamides as N-Glycoprotein Linkage Region An. Chemistry 2013; 19:17720-32. [DOI: 10.1002/chem.201302018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Indexed: 11/09/2022]
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6
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Mathiselvam M, Ramkumar V, Loganathan D, Pérez S. Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: synthesis and X-ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage. Glycoconj J 2013; 31:71-87. [PMID: 24150739 DOI: 10.1007/s10719-013-9504-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/07/2013] [Accepted: 10/07/2013] [Indexed: 11/27/2022]
Abstract
The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, ϕN, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the ϕN value of cellobiosyl analogs deviate ~9° with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18°. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ₂ value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6° to -109.9°). This large span of χ₂ value suggests the greater degree of rotational freedom around C1'-C2' bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions.
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Affiliation(s)
- Manoharan Mathiselvam
- Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036, India,
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7
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Srivastava A, Varghese B, Loganathan D. Synthesis and X-ray crystallographic investigation of N-(α-D-arabinopyranosyl)alkanamides as N-glycoprotein linkage region analogs. Carbohydr Res 2013; 380:92-100. [PMID: 23981855 DOI: 10.1016/j.carres.2013.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/28/2013] [Accepted: 07/29/2013] [Indexed: 01/10/2023]
Abstract
N-Glycoprotein linkage region constituents namely 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and asparagine (Asn) are conserved among all eukaryotes. Earlier crystallographic studies on the linkage region conformation revealed that among all the models and analogs of the N-glycoprotein linkage region, XylβNHAc showed maximum deviation in the ϕN value as compared to the value reported for the model compound, GlcNAcβNHAc. In order to understand the effect of another pentopyranose, viz., arabinose, on the N-glycosidic torsion angles and molecular assembly, three arabinopyranosyl alkanamides were synthesized and their X-ray crystal structures elucidated. A comparative analysis of the N-glycosidic torsion, ϕN of the three analogs revealed the greater rotational freedom around the C1-N1 bond as compared to the GlcNAc derivatives. Molecular assembly of propionamido and chloroacetamido derivatives is characterized by the presence of anti-parallel bilayers of the molecules. This unique molecular assembly is hitherto unknown in all other models and analogs of N-glycoprotein linkage region. This study reveals that N-glycosidic torsions are influenced by the glycan as well as molecular packing.
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Affiliation(s)
- Amrita Srivastava
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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8
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Mathiselvam M, Loganathan D, Varghese B. Synthesis of N-(β-D-glycuronopyranosyl)alkanamides and 1-(β-D-glycuronopyranosyl)-4-phenyl-[1,2,3]-triazoles as N-glycoprotein linkage region analogs: examination of the effect of C5 substituent on the N-glycosidic torsion (ΦN) based on X-ray crystallography. Carbohydr Res 2013; 380:1-8. [PMID: 23896157 DOI: 10.1016/j.carres.2013.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/20/2013] [Accepted: 06/26/2013] [Indexed: 11/30/2022]
Abstract
The torsion angle around the N-glycoprotein linkage region (GlcNAc-Asn) is an important factor for presenting sugar on the cell surface which is crucial for many biological processes. Earlier studies using model and analogs showed that this important torsion angle is greatly influenced by substitutions in the sugar part. In the present work, uronic acid alkanamides and triazole derivatives have been designed and synthesized as newer analogs of N-glycoprotein linkage region to understand the influence of the carboxylic group on linkage region torsion as well as on molecular packing. Crystal structure of N-(β-D-galacturonopyranosyl)acetamide is solved with the space group of P22121. Comparison of the torsion angle and molecular packing of this compound with N-(β-D-galactopyranosyl)acetamide showed that changing the C6-hydoxymethyl group to the carboxylic acid group has minimum influence on the N-glycosidic torsion angle, ΦN and significant influence on the molecular packing.
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Affiliation(s)
- Manoharan Mathiselvam
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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9
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Mathiselvam M, Srivastava A, Varghese B, Pérez S, Loganathan D. Synthesis and X-ray crystallographic investigation of N-(β-d-glycosyl)butanamides derived from GlcNAc and chitobiose as analogs of the conserved chitobiosylasparagine linkage of N-glycoproteins. Carbohydr Res 2013; 380:37-44. [DOI: 10.1016/j.carres.2013.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 07/07/2013] [Accepted: 07/10/2013] [Indexed: 12/01/2022]
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10
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Han C, Zhao J, Yang F, Wang J. Structural Dynamics of N-Propionyl-d-glucosamine Probed by Infrared Spectroscopies and Ab Initio Computations. J Phys Chem A 2013; 117:6105-15. [DOI: 10.1021/jp400096a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chen Han
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
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11
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Srivastava A, Varghese B, Loganathan D. X-Ray Crystallographic Investigation of Fully Acetylated N-(2-Deoxy-2-Acetamido-β-D-Glucopyranosyl)Alkanamides as N-Glycoprotein Linkage Region Analogs. J Carbohydr Chem 2012. [DOI: 10.1080/07328303.2011.631237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Amrita Srivastava
- a Department of Chemistry , Indian Institute of Technology Madras , Chennai , – 600036 , India
| | - Babu Varghese
- b Department of Chemistry, Sophisticated Analytical Instrumentation Facility , Indian Institute of Technology Madras , Chennai , – 600036 , India
| | - Duraikkannu Loganathan
- a Department of Chemistry , Indian Institute of Technology Madras , Chennai , – 600036 , India
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12
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Marcelo F, Cañada FJ, André S, Colombo C, Doro F, Gabius HJ, Bernardi A, Jiménez-Barbero J. α-N-Linked glycopeptides: conformational analysis and bioactivity as lectin ligands. Org Biomol Chem 2012; 10:5916-23. [DOI: 10.1039/c2ob07135e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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Mathiselvam M, Varghese B, Loganathan D. Synthesis and X-ray crystallographic investigation of N-(3-deoxy-3-acetamido-β-D-glycopyranosyl)alkanamides as analogs of N-glycoprotein linkage region. Glycoconj J 2011; 28:573-80. [DOI: 10.1007/s10719-011-9357-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
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14
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Cioci G, Srivastava A, Loganathan D, Mason SA, Pérez S, Imberty A. Low-Temperature Neutron Diffraction Structures of N-Glycoprotein Linkage Models and Analogues: Structure Refinement and Trifurcated Hydrogen Bonds. J Am Chem Soc 2011; 133:10042-5. [DOI: 10.1021/ja203239j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gianluca Cioci
- European Synchrotron Radiation Facility, BP220 Grenoble, France
| | | | | | | | - Serge Pérez
- European Synchrotron Radiation Facility, BP220 Grenoble, France
| | - Anne Imberty
- CERMAV-CNRS (affiliated with Université Joseph Fourier and ICMG), BP53 Grenoble, France
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15
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Fernández-Tejada A, Corzana F, Busto JH, Jiménez-Osés G, Jiménez-Barbero J, Avenoza A, Peregrina JM. Insights into the geometrical features underlying beta-O-GlcNAc glycosylation: water pockets drastically modulate the interactions between the carbohydrate and the peptide backbone. Chemistry 2009; 15:7297-301. [PMID: 19544521 DOI: 10.1002/chem.200901204] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alberto Fernández-Tejada
- Departamento de Química, Universidad de La Rioja, UA-CSIC. Madre de Dios 51, 26006 Logroño, La Rioja, Spain
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Lütteke T. Analysis and validation of carbohydrate three-dimensional structures. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:156-68. [PMID: 19171971 PMCID: PMC2631634 DOI: 10.1107/s0907444909001905] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 01/15/2009] [Indexed: 12/04/2022]
Abstract
Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.
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Affiliation(s)
- Thomas Lütteke
- Bijvoet Centre for Biomolecular Research, BOC2, Utrecht University, Utrecht, The Netherlands.
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17
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Ali MMN, Aich U, Pérez S, Imberty A, Loganathan D. Examination of the effect of structural variation on the N-glycosidic torsion (PhiN) among N-(beta-D-glycopyranosyl)acetamido and propionamido derivatives of monosaccharides based on crystallography and quantum chemical calculations. Carbohydr Res 2008; 344:355-61. [PMID: 19108819 DOI: 10.1016/j.carres.2008.11.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/06/2008] [Accepted: 11/06/2008] [Indexed: 11/24/2022]
Abstract
GlcNAcbetaAsn linkage is conserved in the N-glycoproteins of all eukaryotes. l-Glutamine (Gln), which is a one carbon higher homolog of Asn, is never glycosylated. X-ray crystallographic study of several beta-1-N-acetamido- and propionamido derivatives of monosaccharides has earlier shown that the N-glycosidic torsion, Phi(N), is influenced to a larger extent by the structural variation of the sugar part than that of the aglycon moiety. In order to examine the influence of the carbohydrate pendent groups on the conformational preference of the N-glycosidic linkage with respect to Phi(N,) several models and analogs with gluco and manno configuration have been studied in the present work by computational chemistry. The crystal structure of XylbetaNHPr is reported here and its molecular packing compared with related analogs. The conjunction of combining Crystallographic and computational studies allows to demonstrate the strong influence that the group at C2, and environmental factors particularly inter- and intramolecular interactions involving regular hydrogen bonds and the weak C-H...O contacts, have on the energy preference of the Phi(N) torsion angle.
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18
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Ali MMN, Aich U, Varghese B, Imberty A. Conformational Preferences of the Aglycon Moiety in Models and Analogs of GlcNAc-Asn Linkage: Crystal Structures and ab Initio Quantum Chemical Calculations of N-(β-d-Glycopyranosyl)haloacetamides. J Am Chem Soc 2008; 130:8317-25. [DOI: 10.1021/ja800335m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohamed Mohamed Naseer Ali
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Udayanath Aich
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Babu Varghese
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Anne Imberty
- CERMAV-CNRS (affiliated to Université Joseph Fourier and ICMG), BP 53, 38041 Grenoble cedex 9, France, Department of Chemistry and Sophisticated Analytical Instrumentation Facility, Indian Institute of Technology Madras, Chennai, 600036, India
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Loganathan D, Aich U. Observation of a unique pattern of bifurcated hydrogen bonds in the crystal structures of the N-glycoprotein linkage region models. Glycobiology 2005; 16:343-8. [PMID: 16352615 DOI: 10.1093/glycob/cwj070] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Elucidation of the intra- and intermolecular carbohydrate-protein interactions would greatly contribute toward obtaining a better understanding of the structure-function correlations of the protein-linked glycans. The weak interactions involving C-H...O have recently been attracting immense attention in the domain of biomolecular recognition. However, there has been no report so far on the occurrence of C-H...O hydrogen bonds in the crystal structures of models and analogs of N-glycoproteins. We present herein an analysis of C-H...O interactions in the crystal structures of all N-glycoprotein linkage region models and analogs. The study reveals a cooperative network of bifurcated hydrogen bonds consisting of N-H...O and C-H...O interactions seen uniquely for the models. The cooperative network consists of two antiparallel chains of bifurcated hydrogen bonds, one involving N1-H, C2'-H and O1' of the aglycon moiety and the other involving N2-H, C1-H and O1'' of the sugar. Such bifurcated hydrogen bonds between the core glycan and protein are likely to play an important role in the folding and stabilization of proteins.
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Affiliation(s)
- Duraikkannu Loganathan
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India.
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Chrysina ED, Kosmopoulou MN, Kardakaris R, Bischler N, Leonidas DD, Kannan T, Loganathan D, Oikonomakos NG. Binding of β-d-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies. Bioorg Med Chem 2005; 13:765-72. [PMID: 15653344 DOI: 10.1016/j.bmc.2004.10.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Accepted: 10/18/2004] [Indexed: 11/20/2022]
Abstract
In an attempt to identify a new lead molecule that would enable the design of inhibitors with enhanced affinity for glycogen phosphorylase (GP), beta-D-glucopyranosyl bismethoxyphosphoramidate (phosphoramidate), a glucosyl phosphate analogue, was tested for inhibition of the enzyme. Kinetic experiments showed that the compound was a weak competitive inhibitor of rabbit muscle GPb (with respect to alpha-D-glucose-1-phosphate (Glc-1-P)) with a Ki value of 5.9 (+/-0.1) mM. In order to elucidate the structural basis of inhibition, we determined the structure of GPb complexed with the phosphoramidate at 1.83 A resolution. The complex structure reveals that the inhibitor binds at the catalytic site and induces significant conformational changes in the vicinity of this site. In particular, the 280s loop (residues 282-287) shifts 0.4-4.3 A (main-chain atoms) to accommodate the phosphoramidate, but these conformational changes do not lead to increased contacts between the inhibitor and the protein that would improve ligand binding.
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Affiliation(s)
- Evangelia D Chrysina
- Institute of Organic and Pharmaceutical Chemistry, The National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., 11635 Athens, Greece
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Lakshmanan T, Loganathan D. Enzymatic synthesis of N-glycoprotein linkage region disaccharide mimetics using β-N-acetylhexosaminidases from Aspergillus oryzae and Vigna radiata. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2004.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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