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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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2
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Su P, Tang Z, Wu W. Generalized Kohn‐Sham energy decomposition analysis and its applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1460] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Zhen Tang
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering Xiamen University Xiamen China
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3
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Ong AAL, Toh DFK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase. Biochemistry 2019; 58:1319-1331. [PMID: 30775913 DOI: 10.1021/acs.biochem.8b01313] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Our data suggest that an S residue incorporated into short 8-mer dsRNA-binding PNAs (dbPNAs) can recognize internal Watson-Crick C-G and U-A, and wobble U-G base pairs (but not G-C, A-U, and G-U pairs) in RNA duplexes. The short S-modified PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. Interestingly, replacement of the C residue in an S·C-G triple with a 5-methyl C results in the disruption of the triplex, probably due to a steric clash between S and 5-methyl C. Previously reported PNA E base shows recognition of U-A and A-U pairs, but not a U-G pair. Thus, S-modified dbPNAs may be uniquely useful for the general recognition of RNA U-G, U-A, and C-G pairs. Shortening the succinyl linker of our PNA S monomer by one carbon atom to have a malonyl linker causes a severe destabilization of triplex formation. Our experimental and modeling data indicate that part of the succinyl moiety in a PNA S monomer may serve to expand the S base forming stacking interactions with adjacent PNA bases.
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Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenyu Meng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhen Yuan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore , Singapore , 117604.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore , 639798
| | - Jia Sheng
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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4
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Wang J, Chen J, Li J, An L, Wang Y, Huang Q, Yao L. Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way. Proteins 2018; 86:684-692. [PMID: 29575221 DOI: 10.1002/prot.25495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/07/2018] [Accepted: 03/15/2018] [Indexed: 11/10/2022]
Abstract
A combined experimental and computational study is performed for arginine side chain stacking with the protein α-helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of ∼0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone-backbone h-bonds (i→i-4 and i-3→i-7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the i→i-4 and i-3→i-7 h-bonds, respectively. This cooperativity is supported by a protein α-helices h-bond survey in the pdb databank where stacking shortens the corresponding h-bond distances.
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Affiliation(s)
- Jia Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingfei Chen
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Jingwen Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liaoyuan An
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Yefei Wang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Qingshan Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
| | - Lishan Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China.,Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266061, China
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5
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Giroud M, Ivkovic J, Martignoni M, Fleuti M, Trapp N, Haap W, Kuglstatter A, Benz J, Kuhn B, Schirmeister T, Diederich F. Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: Amide⋅⋅⋅Heteroarene π-Stacking Interactions and Chalcogen Bonding in the S3 Pocket. ChemMedChem 2017; 12:257-270. [DOI: 10.1002/cmdc.201600563] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/19/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Jakov Ivkovic
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Mara Martignoni
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Marianne Fleuti
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wolfgang Haap
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Andreas Kuglstatter
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Jörg Benz
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Bernd Kuhn
- F. Hoffmann-La Roche Ltd.; Pharma Research and Early Development (pRED); Therapeutic Modalities; Roche Innovation Center Basel; Grenzacherstrasse 124 4070 Basel Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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6
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Liu Z, Trindle CO, Gu Q, Wu W, Su P. Unravelling hydrogen bonding interactions of tryptamine–water dimer from neutral to cation. Phys Chem Chem Phys 2017; 19:25260-25269. [DOI: 10.1039/c7cp03491a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The physical origin for the three intermolecular hydrogen bonds in the neutral and cationic forms of the tryptamine–water dimer is explored.
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Affiliation(s)
- Zongyuan Liu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Carl O. Trindle
- Chemistry Department
- University of Virginia
- Charlottesville
- USA
| | - Quanli Gu
- Chemistry Department
- University of Oklahoma
- Norman
- USA
| | - Wei Wu
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
| | - Peifeng Su
- The State Key Laboratory of Physical Chemistry of Solid Surfaces
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and College of Chemistry and Chemical Engineering
- Xiamen University
- Xiamen
- China
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7
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Taimoory SM, Dudding T. An Evolving Insight into Chiral H-Bond Catalyzed Aza-Henry Reactions: A Cooperative Role for Noncovalent Attractive Interactions Unveiled by Density Functional Theory. J Org Chem 2016; 81:3286-95. [PMID: 27008440 DOI: 10.1021/acs.joc.6b00248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of cooperative effects arising from noncovalent attractive interactions as a vital factor governing stereoinduction in chiral H-bond catalyzed aza-Henry reactions is reported. Supporting this finding were density functional theory (DFT) calculations which revealed a shape and size dependency existed between the catalyst and substrates that when matched lead to high enantioselectivity, as reflected by favorable activation parameters. Associated with optimal catalyst and substrate pairing were a closed catalytic binding pocket and a synclinal orientation of the substrates that reinforced favorable stereoelectronic effects and dispersive type forces. Meanwhile, unfavorable steric interactions were found to be a dominant effect controlling diastereoselection.
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Affiliation(s)
| | - Travis Dudding
- Brock University , 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1 Canada
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