1
|
French AD. Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose. Adv Carbohydr Chem Biochem 2021; 80:15-93. [PMID: 34872656 DOI: 10.1016/bs.accb.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.
Collapse
Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana, USA
| |
Collapse
|
2
|
French AD, Montgomery DW, Prevost NT, Edwards JV, Woods RJ. Comparison of cellooligosaccharide conformations in complexes with proteins with energy maps for cellobiose. Carbohydr Polym 2021; 264:118004. [PMID: 33910736 DOI: 10.1016/j.carbpol.2021.118004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/24/2023]
Abstract
Shapes (conformations) of cellulose molecules are described by their glycosidic linkage torsion angles ϕ and ψ. Although the torsions are known for cellulose in crystals, amorphous shapes are also interesting for understanding reactivity and physical properties. ϕ and ψ determination for unorganized matter is difficult; one approach is to study their range in many related molecules. For example, linkage torsions of cellulose should be similar to those in cellobiose. Herein, torsions were measured for cellooligosaccharides and lactose moieties complexed with proteins in the Protein Data Bank (PDB). These torsions were compared with ϕ/ψ maps based on quantum mechanics energies for solvated cellobiose and analogs lacking hydroxyl groups. Most PDB conformations corresponded to low map energies. Amorphous cellulose should be generally extended with individual linkages that would give 2- to 3-fold helices. The map for an analog lacking hydrogen bonding ability was more predictive for PDB linkages than the cellobiose map.
Collapse
Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - David W Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
| | - Nicolette T Prevost
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - J Vincent Edwards
- Southern Regional Research Center, U. S. Department of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA, 70124, USA.
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
| |
Collapse
|
3
|
Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
Collapse
Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
| |
Collapse
|
4
|
Computerized Molecular Modeling of Carbohydrates. Methods Mol Biol 2020. [PMID: 32617954 DOI: 10.1007/978-1-0716-0621-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Computerized molecular modeling continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to computational chemists who do not have a strong background in carbohydrates, and its comments on various methods and studies might be of more use to carbohydrate chemists who are inexperienced with computation. Work on the intrinsic variability of glucose, an overall theme, is described. Other areas of the authors' emphasis, including evaluation of hydrogen bonding by the atoms-in-molecules approach, and validation of modeling methods with crystallographic results are also presented.
Collapse
|
5
|
Gaweda K, Plazinski W. Pyranose ring conformations in mono- and oligosaccharides: a combined MD and DFT approach. Phys Chem Chem Phys 2017; 19:20760-20772. [DOI: 10.1039/c7cp02920a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A two-step computational protocol is proposed to efficiently study the conformational properties of hexopyranoses with a special emphasis on their ring-inversion-properties. By applying it, the errors resulting from overestimating the contribution of the hydrogen bond-rich, low-energy structures that are not abundant in aqueous solutions are avoided.
Collapse
Affiliation(s)
- Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- 30-239 Cracow
- Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry
- Polish Academy of Sciences
- 30-239 Cracow
- Poland
| |
Collapse
|
6
|
Plazinski W, Drach M. The influence of the hexopyranose ring geometry on the conformation of glycosidic linkages investigated using molecular dynamics simulations. Carbohydr Res 2015; 415:17-27. [DOI: 10.1016/j.carres.2015.07.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/20/2015] [Accepted: 07/29/2015] [Indexed: 11/29/2022]
|
7
|
Reilly PJ, Rovira C. Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter J. Reilly
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011-2230, United States
| | - Carme Rovira
- Departament de Química Orgànica
and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| |
Collapse
|
8
|
Computerized Models of Carbohydrates. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
9
|
|
10
|
Yamane C, Miyamoto H, Hayakawa D, Ueda K. Folded-chain structure of cellulose II suggested by molecular dynamics simulation. Carbohydr Res 2013; 379:30-7. [DOI: 10.1016/j.carres.2013.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 05/21/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
|
11
|
Calle L, Roldós V, Cañada FJ, Uhrig ML, Cagnoni AJ, Manzano VE, Varela O, Jiménez-Barbero J. Escherichia coliβ-Galactosidase Inhibitors through Modifications at the Aglyconic Moiety: Experimental Evidence of Conformational Distortion in the Molecular Recognition Process. Chemistry 2013; 19:4262-70. [DOI: 10.1002/chem.201203673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Indexed: 11/07/2022]
|
12
|
Wu M, Nerinckx W, Piens K, Ishida T, Hansson H, Sandgren M, Ståhlberg J. Rational design, synthesis, evaluation and enzyme-substrate structures of improved fluorogenic substrates for family 6 glycoside hydrolases. FEBS J 2012; 280:184-98. [DOI: 10.1111/febs.12060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/31/2012] [Accepted: 11/05/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Miao Wu
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Wim Nerinckx
- Laboratory for Protein Biochemistry and Biomolecular Engineering; Department of Biochemistry and Microbiology; University of Gent; Gent; Belgium
| | | | - Takuya Ishida
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Henrik Hansson
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Mats Sandgren
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| | - Jerry Ståhlberg
- Department of Molecular Biology; Swedish University of Agricultural Sciences; Uppsala; Sweden
| |
Collapse
|
13
|
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: 75] [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.
Collapse
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
| |
Collapse
|
14
|
Naidoo KJ. Multidimensional free energy volumes offer unique insights into reaction mechanisms, molecular conformation and association. Phys Chem Chem Phys 2012; 14:9026-36. [DOI: 10.1039/c2cp23802k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
15
|
French AD. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose. Adv Carbohydr Chem Biochem 2012; 67:19-93. [PMID: 22794182 DOI: 10.1016/b978-0-12-396527-1.00002-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
16
|
Abstract
Computerized molecular modeling continues to increase in capability and applicability to carbohydrates. This chapter covers nomenclature and conformational aspects of carbohydrates, perhaps of greater use to carbohydrate-inexperienced computational chemists. Its comments on various methods and studies might be of more use to computation-inexperienced carbohydrate chemists. New work on intrinsic variability of glucose, an overall theme, is described.
Collapse
|
17
|
Barnett CB, Naidoo KJ. Ring puckering: a metric for evaluating the accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB carbohydrate QM/MM simulations. J Phys Chem B 2010; 114:17142-54. [PMID: 21138284 DOI: 10.1021/jp107620h] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The puckered conformations of furanose and pyranose carbohydrate rings are central to analyzing the action of enzymes on carbohydrates. Enzyme reaction mechanisms are generally inaccessible to experiments and so have become the focus of QM(semiempirical)/MM simulations. We show that the complete free energy of puckering is required to evaluate the accuracy of semiempirical methods used to study reactions involving carbohydrates. Interestingly, we find that reducing the free energy space to lower dimensions results in near meaningless minimum energy pathways. We analyze the furanose and pyranose free energy pucker surfaces and volumes using AM1, PM3, PM3CARB-1, and SCC-DFTB. A comparison with DFT optimized structures and a HF free energy surface reveals that SCC-DFTB provides the best semiempirical description of five- and six-membered carbohydrate ring deformation.
Collapse
Affiliation(s)
- Christopher B Barnett
- Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | | |
Collapse
|