1
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Scheiner S, Derewenda ZS. Differing Effects of Nonlinearity around the Proton Acceptor on CH··O and NH··O H-Bond Strength within Proteins. J Phys Chem B 2024. [PMID: 39024061 DOI: 10.1021/acs.jpcb.4c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The effects of deviations from nonlinearity around the carbonyl proton acceptor of an amide group are assessed by DFT quantum chemical calculations for both CH··O and NH··O H-bonds. The proton donors are the imidazole functional group of His and the indole of Trp, which are paired respectively with N-methylacetamide and acetamide. The displacement of either CH or NH group toward the carbonyl O sp2 lone pairs stabilizes the system and strengthens the H-bond. But the two donor groups differ in their response to a shift out of the amide plane. While the NH··O H-bond is weakened by this displacement, a substantial strengthening is observed when the CH donor is moved out of this plane, in one direction versus the other. This pattern is explained on the basis of simple Coulombic considerations.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| | - Zygmunt S Derewenda
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908-0736, United States
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2
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Szczygiel M, Derewenda U, Scheiner S, Minor W, Derewenda ZS. A structural role for tryptophan in proteins, and the ubiquitous Trp C δ1-H...O=C (backbone) hydrogen bond. Acta Crystallogr D Struct Biol 2024; 80:551-562. [PMID: 38941144 PMCID: PMC11220837 DOI: 10.1107/s2059798324005515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/09/2024] [Indexed: 06/29/2024] Open
Abstract
Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nϵ-H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1-H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C-H...O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C-H group. Consequently, Cα-H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cϵ1-H and Cδ2-H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1-H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1-H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5-3.0 kcal mol-1, depending on the specific stereochemistry.
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Affiliation(s)
- Michal Szczygiel
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Urszula Derewenda
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
| | - Zygmunt S. Derewenda
- Department of Molecular Physiology and Biological PhysicsUniversity of Virginia1340 Jefferson Park AvenueCharlottesvilleVA22908-0736USA
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3
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Hofmaier M, Heger JE, Lentz S, Schwarz S, Müller-Buschbaum P, Scheibel T, Fery A, Müller M. Influence of the Sequence Motive Repeating Number on Protein Folding in Spider Silk Protein Films. Biomacromolecules 2023; 24:5707-5721. [PMID: 37934893 DOI: 10.1021/acs.biomac.3c00688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Like multiblock copolymers, spider silk proteins are built of repetitive sequence motives. One prominent repetitive motif is based on the consensus sequence of spidroin 4 of the spider Araneus diadematus ADF4. The number x of the repeating sequence motives (C) determines the molecular weight of the recombinant ADF4-based, engineered spider silk protein denoted as eADF4(Cx). eADF4(Cx) can be used as a model for intrinsically disordered proteins (IDP) and to elucidate their folding. Herein, the influence of the variation of the sequence motive repeating number x (x = 1, 2, 4, 8, 16) on the protein folding within eADF4(Cx) films was investigated. eADF4(Cx) films were cast from 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) solutions onto planar silicon model substrates, revealing mainly helical or random coil structure. Upon treatment with methanol vapor (ptm), the formation of crystalline β-sheets was triggered. Dichroic Fourier-transform infrared (FTIR) spectroscopy, circular dichroism, spectroscopic ellipsometry, atomic force microscopy, grazing-incidence small-angle X-ray scattering (GISAXS), grazing-incidence wide-angle X-ray scattering (GIWAXS), and electrokinetic and contact angle measurements were used to get information concerning the secondary structure and folding kinetics, orientation of β-sheets, the ratio of parallel/antiparallel β-sheets, domain sizes and distributions, surface topography, surface potential, hydrophobicity and the film integrity under water. Significant differences in the final β-sheet content, the share of antiparallel β-sheet structures, film integrity, surface potential, and isoelectric points between eADF4(Cx) with x = 1, 2 and eADF4(Cx) with x = 4, 8, 16 gave new insights in the molecular weight-dependent structure formation and film properties of IDP systems. GISAXS and kinetic measurements confirmed a relation between β-sheet crystal growth rate and final β-sheet crystal size. Further, competing effects of reduced diffusibility hindering accelerated crystal growth and enhanced backfolding promoting accelerated crystal growth with increasing molecular weight were discussed.
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Affiliation(s)
- Mirjam Hofmaier
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), Dresden 01069, Germany
| | - Julian E Heger
- TUM School of Natural Sciences, Department of Physics, Chair for Functional Materials, Technical University of Munich, Garching 85748, Germany
| | - Sarah Lentz
- Functional Polymer Interfaces Group, University of Bayreuth, Bayreuth 95447, Germany
| | - Simona Schwarz
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
| | - Peter Müller-Buschbaum
- TUM School of Natural Sciences, Department of Physics, Chair for Functional Materials, Technical University of Munich, Garching 85748, Germany
- Heinz Maier-Leibnitz Zentrum (MLZ), Technical University of Munich, Garching 85748, Germany
| | - Thomas Scheibel
- Chair of Biomaterials, University of Bayreuth, Bayreuth 95447, Germany
- Bayreuth Center of Colloids and Interfaces (BZKG), University of Bayreuth, Bayreuth 95440, Germany
- Bayreuth Center for Molecular Bioscience (BZMB), University of Bayreuth, Bayreuth 95440, Germany
- Bayreuth Center for Material Science and Engineering (BayMAT), Universität Bayreuth, Bayreuth 95440, Germany
- Bavarian Polymer Institute (BPI), University of Bayreuth, Bayreuth 95440, Germany
| | - Andreas Fery
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Physical Chemistry of Polymeric Materials, Technical University Dresden (TUD), Dresden 01069, Germany
| | - Martin Müller
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden (IPF), Dresden 01069, Germany
- Chair of Macromolecular Chemistry, Technical University of Dresden (TUD), Dresden 01062, Germany
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4
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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5
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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6
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Zhang Y, Li Q, Wu H, Wang Y, Wang Y, Rencus-Lazar S, Zhao Y, Wang J, Mei D, Xu H, Gazit E, Tao K. Racemic Amino Acid Assembly Enables Supramolecular β-Sheet Transition with Property Modulations. ACS NANO 2023; 17:2737-2744. [PMID: 36696300 DOI: 10.1021/acsnano.2c11006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Amino acids are the most simplistic bio-building blocks and perform a variety of functions in metabolic activities. Increasing publications report that amino acid-based superstructures present amyloid-like characteristics, arising from their supramolecular β-sheet secondary structures driven by hydrogen-bonding-connected supramolecular β-strands, which are formed by head-to-tail hydrogen bonds between terminal amino and carboxyl groups of the adjacent residues. Therefore, the establishment of the structure-function relationships is critical for exploring the properties and applications of amino acid assemblies. Among the naturally encoded self-assembling amino acids, tyrosine (Y)-based superstructures have been found to show diverse properties and functions including high rigidity, promoting melanin formations, mood regulations, and preventing anxiety, thus showing promising potential as next-generation functional biomaterials for biomedical and bio-machine interface applications. However, the development of Y-based organizations of functional features is severely limited due to the intrinsic difficulty of modulating the energetically stable supramolecular β-sheet structures. Herein, we report that by the racemic assembly of l-Y and d-Y, the supramolecular secondary structures are modulated from the antiparallel β-sheets in the enantiomeric assemblies to the parallel ones in the racemate counterparts, thus leading to higher degrees of freedom, which finally induce distinct organization kinetics and modulation of the physicochemical properties including the optical shifts, elastic softening, and the piezoelectric outputs of the superstructures.
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Affiliation(s)
- Yan Zhang
- Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Qi Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing100190, China
| | - Haoran Wu
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou311200, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou311200, China
| | - Yancheng Wang
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
| | - Yan Wang
- Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Sigal Rencus-Lazar
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou311200, China
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yurong Zhao
- Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Jiqian Wang
- Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Deqing Mei
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
| | - Hai Xu
- Department of Biological and Energy Chemical Engineering, College of Chemical Engineering, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao266580, China
| | - Ehud Gazit
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou311200, China
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801, Tel Aviv, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Kai Tao
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou311200, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Key Laboratory of Advanced Manufacturing Technology of Zhejiang Province, School of Mechanical Engineering, Zhejiang University, Hangzhou310030, China
- Zhejiang-Israel Joint Laboratory of Self-Assembling Functional Materials, Hangzhou311200, China
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7
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Asghar S, Hameed S, Tahir MN, Naseer MM. Molecular duplexes featuring NH···N, CH···O and CH···π interactions in solid-state self-assembly of triazine-based compounds. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220603. [PMID: 36397969 PMCID: PMC9626258 DOI: 10.1098/rsos.220603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Synthetic supramolecular structures constructed through the cooperative action of numerous non-covalent forces are highly desirable as models to unravel and understand the complexity of systems created in nature via self-assembly. Taking advantage of the low cost of 2,4,6-trichloro-1,3,5-triazine (cyanuric chloride) and the sequential nucleophilic substitution reactions with almost all types of nucleophiles, a series of six structurally related novel s-triazine derivatives 1-6 were synthesized and structurally characterized based on their physical, spectral and crystallographic data. The solid-state structures of all the six compounds showed intriguing and unique molecular duplexes featuring NH···N, CH···O and CH···π interactions. Careful analysis of different geometric parameters of the involved H-bonds indicates that they are linear, significant and are therefore responsible for guiding the three-dimensional structure of these compounds in the solid state. The prevalence of sextuple hydrogen bond array-driven molecular duplexes and the possibility of structural modifications on the s-triazine ring render these novel triazine derivatives 1-6 attractive as a platform to create heteroduplex constructs and their subsequent utility in the field of supramolecular chemistry and crystal engineering.
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Affiliation(s)
- Shazia Asghar
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
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8
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Pan H, Pei F, Ma G, Ma N, Zhong L, Zhao L, Hu Q. 3D printing properties of Flammulina velutipes polysaccharide-soy protein complex hydrogels. J FOOD ENG 2022. [DOI: 10.1016/j.jfoodeng.2022.111170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Steinert RM, Kasireddy C, Heikes ME, Mitchell-Koch KR. Newly identified C–H⋯O hydrogen bond in histidine. Phys Chem Chem Phys 2022; 24:19233-19251. [DOI: 10.1039/d2cp02048c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).
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Affiliation(s)
- Ryan M. Steinert
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Chandana Kasireddy
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Micah E. Heikes
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Katie R. Mitchell-Koch
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
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10
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An NT, Duong NT, Tri NN, Trung NT. Role of O–H⋯O/S conventional hydrogen bonds in considerable C sp2–H blue-shift in the binary systems of acetaldehyde and thioacetaldehyde with substituted carboxylic and thiocarboxylic acids. RSC Adv 2022; 12:35309-35319. [DOI: 10.1039/d2ra05391h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/27/2022] [Indexed: 12/13/2022] Open
Abstract
The presence of O–H⋯O/S conventional hydrogen bonds in the complex governs a significant blue shift of Csp2–H bonds.
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Affiliation(s)
- Nguyen Truong An
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam
| | - Nguyen Thi Duong
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam
| | - Nguyen Ngoc Tri
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam
- Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, Quy Nhon, Vietnam
| | - Nguyen Tien Trung
- Faculty of Natural Sciences, Quy Nhon University, Quy Nhon, Vietnam
- Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University, Quy Nhon, Vietnam
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11
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Unravelling the non-covalent interactions in certain n-propyl amine – Ether systems through acoustic and DFT studies at 303.15 K. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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12
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Verma N, Tao Y, Kraka E. Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes. J Phys Chem B 2021; 125:2551-2565. [DOI: 10.1021/acs.jpcb.0c11392] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Niraj Verma
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
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14
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Abstract
A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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16
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Xia J, Zhu Y, He Z, Wang F, Wu H. Superstrong Noncovalent Interface between Melamine and Graphene Oxide. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17068-17078. [PMID: 30998319 DOI: 10.1021/acsami.9b02971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
There have been growing academic interests in the study of strong organic molecule-graphene [or graphene oxide (GO)] systems, owing to their essential noncovalent nature and the consequent chemomechanical behavior within the interface. A more recent experimental measurement [ Chem 2018, 4, 896-910] reported that the melamine-GO interface exhibits a remarkable noncovalent binding strength up to ∼1 nN, even comparable with typical covalent bonds. But the poor understanding on the complex noncovalent nature in particular makes it challenging to unveil the mystery of this high-performance interface. Herein, we carry out first-principles calculations to investigate the atomistic origin of ultrastrong noncovalent interaction between the melamine molecule and the GO sheet, as well as the chemomechanical synergy in interfacial behavior. The anomalous O-H···N hydrogen bonding, formed between the triazine moiety of melamine and the -OH in GO, is found cooperatively enhanced by the pin-like NH2-π interaction, which is responsible for the strong interface. Following static pulling simulations validates the 1 nN level rupture strength and the contribution of each noncovalent interaction within the interface. Moreover, our results show that the -OH hydrogen bonding will mainly augment the interfacial adhesion strength, whereas the -NH2 group cooperating with the -OH hydrogen bonding and conjugating with the GO surface will greatly improve the interfacial shear performance. Our work deepens the understanding on the chemomechanical behaviors within the noncovalent interface, which is expected to provide new potential strategies in designing high-performance graphene-based artificial nacreous materials.
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Affiliation(s)
- Jun Xia
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics , University of Science and Technology of China , Hefei 230027 , China
| | - YinBo Zhu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics , University of Science and Technology of China , Hefei 230027 , China
| | - ZeZhou He
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics , University of Science and Technology of China , Hefei 230027 , China
| | - FengChao Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics , University of Science and Technology of China , Hefei 230027 , China
| | - HengAn Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, CAS Center for Excellence in Complex System Mechanics , University of Science and Technology of China , Hefei 230027 , China
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17
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Ghosh S, Wategaonkar S. C–H···O Hydrogen Bond Anchored Water Bridge in 1,2,4,5-Tetracyanobenzene-Water Clusters. J Phys Chem A 2019; 123:3851-3862. [DOI: 10.1021/acs.jpca.9b02238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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18
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Chernyshov IY, Vener MV, Shenderovich IG. Local-structure effects on 31P NMR chemical shift tensors in solid state. J Chem Phys 2019; 150:144706. [PMID: 30981271 DOI: 10.1063/1.5075519] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The effect of the local structure on the 31P NMR chemical shift tensor (CST) has been studied experimentally and simulated theoretically using the density functional theory gauge-independent-atomic-orbital approach. It has been shown that the dominating impact comes from a small number of noncovalent interactions between the phosphorus-containing group under question and the atoms of adjacent molecules. These interactions can be unambiguously identified using the Bader analysis of the electronic density. A robust and computationally effective approach designed to attribute a given experimental 31P CST to a certain local morphology has been elaborated. This approach can be useful in studies of surfaces, complex molecular systems, and amorphous materials.
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Affiliation(s)
- Ivan Yu Chernyshov
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Mikhail V Vener
- Department of Quantum Chemistry, D. Mendeleev University of Chemical Technology, Moscow 125047, Russia
| | - Ilya G Shenderovich
- Institute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany
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19
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Mohammed Hussain S, Kumar R, Mohamed Naseer Ali M, Kannappan V. Structural effect on the strength of non-covalent interactions in binary mixtures of benzyl amine and certain ethers through ultrasonic, FT-IR spectral and DFT studies at 303.15 K. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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α-methylation and α-fluorination electronic effects on the regioselectivity of carbonyl groups of uracil by H and triel bonds in the interaction of U, T and 5FU with HCl and TrH 3 (Tr = B, Al). J Mol Graph Model 2019; 88:237-246. [PMID: 30772654 DOI: 10.1016/j.jmgm.2019.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/23/2022]
Abstract
Quantum chemical calculations at the ωB97XD/6-311++G(d,p) level of theory have been executed to investigate the effect of substituents via hydrogen-bonded and triel-bonded complexes between uracil (U), thymine (T) and 5-fluorouracil (5FU) with HCl for the former complexes, and with BH3 and AlH3 for the latter complexes. These calculations are supported by single-point energy calculations at MP2/6-311++G(d,p) and CCSD/6-31 + G(d,p) levels of theory, Natural Bond Orbital (NBO) and Molecular Electrostatic Potentials (MEPs) analyses, and global/local reactivity descriptors. The results reveal that triel-bonded complexes are strongly bounded than hydrogen-bonded ones, and Al-containing dimers stronger than B-containing ones. In addition, as the central triel atom grows in size, B-containing dimers (B-O triel bond) are accompanied by weak B-H⋯O unconventional H-bonds. According to local reactivity descriptors, the B-O triel bond is hard-hard interaction that indicates that the association is primarily charge controlled, while the Al-O triel bond is soft-soft interaction that is primarily orbital controlled. In both Hydrogen as well as triel-bonded complexes, the α-methylation slightly overestimates the binding strength of U, while the α-fluorination exerts the opposite role by underestimating the binding strength of U. In overall, the effect of substituents on the bond strength and thus on the regioselectivity is very small, suggesting a competition between the two carbonyl groups in terms of structures and binding energies.
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21
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Churakov AV, Grishanov DA, Medvedev AG, Mikhaylov AA, Tripol'skaya TA, Vener MV, Navasardyan MA, Lev O, Prikhodchenko PV. Cyclic dipeptide peroxosolvates: first direct evidence for hydrogen bonding between hydrogen peroxide and a peptide backbone. CrystEngComm 2019. [DOI: 10.1039/c9ce00892f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystal structures of cyclic dipeptide peroxosolvates provide valuable insight into the non-redox interaction of hydrogen peroxide with the peptide backbone.
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Affiliation(s)
- Andrei V. Churakov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Dmitry A. Grishanov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexander G. Medvedev
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Alexey A. Mikhaylov
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Tatiana A. Tripol'skaya
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Mikhail V. Vener
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
- Department of Quantum Chemistry
| | - Mger A. Navasardyan
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
| | - Ovadia Lev
- The Casali Center of Applied Chemistry
- The Institute of Chemistry
- The Hebrew University of Jerusalem
- Jerusalem 91904
- Israel
| | - Petr V. Prikhodchenko
- Kurnakov Institute of General and Inorganic Chemistry
- Russian Academy of Sciences
- Moscow 119991
- Russia
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22
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Vibhute AM, Deva Priyakumar U, Ravi A, Sureshan KM. Model molecules to classify CHO hydrogen-bonds. Chem Commun (Camb) 2018; 54:4629-4632. [PMID: 29671427 DOI: 10.1039/c8cc01653d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We developed a set of conformationally locked molecules each of which makes a single CHO H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CHO H-bond varied from 0.93-1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CHO H-bond strengths quantified using a computational method.
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Affiliation(s)
- Amol M Vibhute
- School of Chemistry, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala-695551, India.
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23
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Surov AO, Voronin AP, Vener MV, Churakov AV, Perlovich GL. Specific features of supramolecular organisation and hydrogen bonding in proline cocrystals: a case study of fenamates and diclofenac. CrystEngComm 2018. [DOI: 10.1039/c8ce01458b] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New zwitterionic cocrystals of fenamate drugs and diclofenac with the naturally occurring amino acid l-proline have been obtained and thoroughly characterised by a variety of experimental and theoretical techniques.
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Affiliation(s)
- Artem O. Surov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | - Alexander P. Voronin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
| | | | - Andrei V. Churakov
- N.S. Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences
- Moscow
- Russia
| | - German L. Perlovich
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
- 153045 Ivanovo
- Russia
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24
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Memarian HR, Kalantari M, Sabzyan H. NMR and DFT Studies of 2-Oxo-1,2,3,4-tetrahydropyridines: Solvent and Temperature Effects. Aust J Chem 2018. [DOI: 10.1071/ch18018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Various 5-carboethoxy-2-oxo-1,2,3,4-tetrahydropyridines and their corresponding oxidation products containing methoxy or nitro groups on different positions of the C4-aryl ring were synthesized and the effect of steric and electrostatic interactions of these aryl substituents on the characteristic peaks in 1H NMR spectra were investigated. In addition, the intermolecular interaction of the parent compound and its oxidized form with solvent was experimentally investigated. For this, 1H NMR spectra of these compounds at different concentrations and temperatures in [D6]DMSO and CDCl3 were investigated. For comparison of the dimerization ability of these heterocyclic compounds with different conformations, the binding electronic energies, the total enthalpies and free energies of dimerization in the gas and solution phases, and the QTAIM (quantum theory of atoms-in-molecules) analysis were determined. These interactions were also studied using density functional theory at the B3LYP/6–311++G(d,p) level. The theoretical results are in good agreement with the experimental results and indicate that the electronic effect of the methoxy and nitro groups on the C4-aryl ring influences the electron density of the heterocyclic ring via the σ bond and, consequently, the chemical shift of the heterocyclic ring protons.
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25
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Assessment of the Presence and Strength of H-Bonds by Means of Corrected NMR. Molecules 2016; 21:molecules21111426. [PMID: 27801801 PMCID: PMC6274571 DOI: 10.3390/molecules21111426] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 11/30/2022] Open
Abstract
The downfield shift of the NMR signal of the bridging proton in a H-bond (HB) is composed of two elements. The formation of the HB causes charge transfer and polarization that lead to a deshielding. A second factor is the mere presence of the proton-accepting group, whose electron density and response to an external magnetic field induce effects at the position of the bridging proton, exclusive of any H-bonding phenomenon. This second positional shielding must be subtracted from the full observed shift in order to assess the deshielding of the proton caused purely by HB formation. This concept is applied to a number of H-bonded systems, both intramolecular and intermolecular. When the positional shielding is removed, the remaining chemical shift is in much better coincidence with other measures of HB strength.
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26
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Driver RW, Claridge TDW, Scheiner S, Smith MD. Torsional and Electronic Factors Control the C-H⋅⋅⋅O Interaction. Chemistry 2016; 22:16513-16521. [PMID: 27709689 PMCID: PMC5113693 DOI: 10.1002/chem.201602905] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Indexed: 01/07/2023]
Abstract
The precise role of non‐conventional hydrogen bonds such as the C−H⋅⋅⋅O interaction in influencing the conformation of small molecules remains unresolved. Here we survey a series of β‐turn mimetics using X‐ray crystallography and NMR spectroscopy in conjunction with quantum calculation, and conclude that favourable torsional and electronic effects are important for the population of states with conformationally influential C−H⋅⋅⋅O interactions. Our results also highlight the challenge in attempting to deconvolute a myriad of interdependent noncovalent interactions in order to focus on the contribution of a single one. Within a small molecule that is designed to resemble the complexity of the environment within peptides and proteins, the interplay of different steric burdens, hydrogen‐acceptor/‐donor properties and rotational profiles illustrate why unambiguous conclusions based solely on NMR chemical shift data are extremely challenging to rationalize.
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Affiliation(s)
- Russell W Driver
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA.
| | - Martin D Smith
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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27
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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28
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Lu N, Chung WC, Ley RM, Lin KY, Francisco JS, Negishi EI. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond. J Phys Chem A 2016; 120:1307-15. [PMID: 26855203 DOI: 10.1021/acs.jpca.6b00144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.
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Affiliation(s)
- Norman Lu
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States.,Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Wei-Cheng Chung
- Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Rebecca M Ley
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States
| | - Kwan-Yu Lin
- Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Joseph S Francisco
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States.,Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Ei-Ichi Negishi
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States
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29
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Bandyopadhyay A, Misra R, Gopi HN. Structural features and molecular aggregations of designed triple-stranded β-sheets in single crystals. Chem Commun (Camb) 2016; 52:4938-41. [DOI: 10.1039/c6cc00127k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Design, synthesis, single-crystal conformations and molecular aggregations of hybrid triple-stranded β-sheets, and their structural analogy with protein structures are reported.
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Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Rajkumar Misra
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
| | - Hosahudya N. Gopi
- Department of Chemistry
- Indian Institute of Science Education and Research-Pune
- Pune
- India
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30
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31
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Estimation of individual NH···X (X = N, O) hydrogen bonding energies in some complexes involving multiple hydrogen bonds using NBO calculations. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1738-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study. CRYSTALS 2015. [DOI: 10.3390/cryst5030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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33
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Brela MZ, Wójcik MJ, Boczar M, Witek Ł, Yasuda M, Ozaki Y. Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds. J Phys Chem B 2015; 119:7922-30. [DOI: 10.1021/acs.jpcb.5b02777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mateusz Z. Brela
- Research
Group of Molecular Modelling of Catalytic Processes, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek J. Wójcik
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Marek Boczar
- Laboratory
of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Łukasz Witek
- Photochemistry
and Luminescence Research Group, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
| | - Mitsuru Yasuda
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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34
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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35
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Maffucci I, Pellegrino S, Clayden J, Contini A. Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids. J Phys Chem B 2015; 119:1350-61. [PMID: 25528885 DOI: 10.1021/jp510775e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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36
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Lee JH, Park HS, Kang YK. Conformational preferences of β-sheet structures in cyclopropane-containing γ-peptides. NEW J CHEM 2015. [DOI: 10.1039/c5nj00545k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligo-γ-peptides based on 2-(aminomethyl)cyclopropanecarboxylic acid (γAmc3) with a cyclopropane constraint on the Cα–Cβ bond preferentially formed parallel β-sheets rather than antiparallel β-sheets due to the stronger N–H⋯O H-bonds in the parallel conformation.
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Affiliation(s)
- Ji Hyang Lee
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
| | - Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 690-708
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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37
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Hao JJ, Wang CS. Rapid evaluation of the interaction energies for carbohydrate-containing hydrogen-bonded complexes via the polarizable dipole–dipole interaction model combined with NBO or AM1 charge. RSC Adv 2015. [DOI: 10.1039/c4ra12814a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The polarizable dipole–dipole interaction model has been developed to rapidly and accurately estimate the hydrogen bond distances and interaction energies for carbohydrate-containing hydrogen-bonded complexes.
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Affiliation(s)
- Jiao-Jiao Hao
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- P. R. China
| | - Chang-Sheng Wang
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- P. R. China
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38
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Brovarets’ OO, Yurenko YP, Hovorun DM. The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation. J Biomol Struct Dyn 2014; 33:1624-52. [DOI: 10.1080/07391102.2014.968623] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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39
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Identification of an ideal-like fingerprint for a protein fold using overlapped conserved residues based approach. Sci Rep 2014; 4:5643. [PMID: 25008052 PMCID: PMC4090624 DOI: 10.1038/srep05643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/19/2014] [Indexed: 02/04/2023] Open
Abstract
Design of an efficient fingerprint that detects homologous proteins at distant sequence identity has been a great challenge. This paper proposes a strategy to extract an ideal-like fingerprint with high specificity and sensitivity from a group of sequences related to a fold. The approach is devised based on the assumptions that the critical residues for a protein fold may be conserved in three aspects, i.e. sequence, structure, and intramolecular interaction, and embedded in secondary structures. We hypothesized that the residues satisfying such conditions simultaneously may work as an efficient fingerprint. This idea was tested on protein folds of various classes, such as beta-strand rich, alpha + beta proteins and alpha/beta proteins with discrete sequence similarities. The fingerprint for each fold was generated by selecting the overlapped conserved residues (OCR) from the conserved residues obtained using independent three alignment methods, i.e. multiple sequence alignment, structure-based alignment, and alignment based on the interstrand hydrogen-bonds. The OCR fingerprints showed more than 90% detection efficiency for all the folds tested and were identified to be almost the minimal fingerprints composed of only critical residues. This study is expected to provide an important conceptual improvement in the identification or design of ideal fingerprints for a protein fold.
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41
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Manin AN, Voronin AP, Manin NG, Vener MV, Shishkina AV, Lermontov AS, Perlovich GL. Salicylamide cocrystals: screening, crystal structure, sublimation thermodynamics, dissolution, and solid-state DFT calculations. J Phys Chem B 2014; 118:6803-14. [PMID: 24861612 DOI: 10.1021/jp5032898] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new cocrystal of 2-hydroxybenzamide (A) with 4-acetamidobenzoic acid (B) has been obtained by the DSC screening method. Thermophysical analysis of the aggregate [A:B] has been conducted and a fusion diagram has been plotted. Cocrystal formation from melts was studied by using thermomicroscopy. A cocrystal single-crystal was grown and its crystal structure was determined. The pattern of noncovalent interactions has been quantified using the solid-state DFT computations coupled with the Bader analysis of the periodic electron density. The sublimation processes of A-B cocrystal have been studied and its thermodynamic functions have been calculated. The classical method of substance transfer by inert gas-carrier was chosen to investigate sublimation processes experimentally. The lattice energy is found to be 143 ± 4 kJ/mol. It is lower than the sum of the corresponding values of the cocrystal pure components. The theoretical value of the lattice energy, 156 kJ/mol, is in reasonable agreement with the experimental one. A ternary phase diagram of solubility (A-B-ethanol) has been plotted and the areas with solutions for growing thermodynamically stable cocrystals have been determined.
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Affiliation(s)
- Alex N Manin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences , 1, Academicheskaya, 153045 Ivanovo, Russia
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42
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Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Reaction between [Ir(COD)(PMe3)3]Cl and 2-aminopent-4-enoic acid: Tridentate N, O and C bonding. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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44
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Kasende OE, Matondo A, Muzomwe M, Muya JT, Scheiner S. Interaction between temozolomide and water: Preferred binding sites. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Sun CL, Ding F, Ding YL, Li Y. The effect of water molecules upon the hydrogen-bonding cooperativity of three-stranded antiparallel β-sheet models. RSC Adv 2014. [DOI: 10.1039/c3ra45892j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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46
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Veljković DŽ, Medaković VB, Andrić JM, Zarić SD. C–H/O interactions of nucleic bases with a water molecule: a crystallographic and quantum chemical study. CrystEngComm 2014. [DOI: 10.1039/c4ce00595c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C–H/O interactions of nucleic bases are substantially stronger than the C–H/O interactions of benzene and pyridine. These results can be very important for molecular recognition of DNA and RNA.
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Affiliation(s)
- D. Ž. Veljković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
| | - J. M. Andrić
- Innovation Center
- Department of Chemistry
- 11000 Belgrade, Serbia
| | - S. D. Zarić
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade, Serbia
- Department of Chemistry
- Texas A&M University at Qatar
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47
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Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Chang-Sheng Wang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
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48
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Buczek A, Broda MA. DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule. Mol Phys 2013. [DOI: 10.1080/00268976.2013.847979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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49
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Horowitz S, Dirk LMA, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc 2013; 135:15536-48. [PMID: 24093804 DOI: 10.1021/ja407140k] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
S-adenosylmethionine (AdoMet)-based methylation is integral to metabolism and signaling. AdoMet-dependent methyltransferases belong to multiple distinct classes and share a catalytic mechanism that arose through convergent evolution; however, fundamental determinants underlying this shared methyl transfer mechanism remain undefined. A survey of high-resolution crystal structures reveals that unconventional carbon-oxygen (CH···O) hydrogen bonds coordinate the AdoMet methyl group in different methyltransferases irrespective of their class, active site structure, or cofactor binding conformation. Corroborating these observations, quantum chemistry calculations demonstrate that these charged interactions formed by the AdoMet sulfonium cation are stronger than typical CH···O hydrogen bonds. Biochemical and structural studies using a model lysine methyltransferase and an active site mutant that abolishes CH···O hydrogen bonding to AdoMet illustrate that these interactions are important for high-affinity AdoMet binding and transition-state stabilization. Further, crystallographic and NMR dynamics experiments of the wild-type enzyme demonstrate that the CH···O hydrogen bonds constrain the motion of the AdoMet methyl group, potentially facilitating its alignment during catalysis. Collectively, the experimental findings with the model methyltransferase and structural survey imply that methyl CH···O hydrogen bonding represents a convergent evolutionary feature of AdoMet-dependent methyltransferases, mediating a universal mechanism for methyl transfer.
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Affiliation(s)
- Scott Horowitz
- Howard Hughes Medical Institute , Ann Arbor, Michigan 48109, United States
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50
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Adhikari U, Scheiner S. First steps in growth of a polypeptide toward β-sheet structure. J Phys Chem B 2013; 117:11575-83. [PMID: 24028425 DOI: 10.1021/jp406326h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The full conformational energy surface is examined for a molecule in which a dipeptide is attached to the same spacer group as another peptide chain, so as to model the seminal steps of β-sheet formation. This surface is compared with the geometrical preferences of the isolated dipeptide to extract the perturbations induced by interactions with the second peptide strand. These interpeptide interactions remove any tendency of the dipeptide to form a C5 ring structure, one of its two normally stable geometries. A C7 structure, the preferred conformation of the isolated dipeptide, remains as the global minimum in the full molecule. However, the stability of this structure is highly dependent upon interpeptide H-bonds with the second chain. The latter forces include not only the usual NH···O interaction, but also a pair of CH···O H-bonds. The secondary minimum is also of C7 type and likewise depends in part upon CH···O H-bonds for its stability. The latter interactions also play a part in the tertiary minimum. A two-strand β-sheet structure is not yet in evidence for this small model system, requiring additional peptide units to be added to each chain.
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Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University , Logan, Utah 84322-0300, United States
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