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Yamasaki K, Tsuzuki S, Tateno H. Stabilization of the Protein Structure by the Many-Body Cooperative Effect in the NH/π Hydrogen-bonding Tryptophan Triad. J Phys Chem B 2024; 128:7401-7406. [PMID: 39018377 DOI: 10.1021/acs.jpcb.4c02391] [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: 07/19/2024]
Abstract
The indole ring of tryptophan can form NH/π hydrogen bonds, acting both as a hydrogen donor at the NH group in the pyrrole subring and as a hydrogen acceptor at the benzene subring. In the structural core of the trimeric stable protein Pholiota squarrosa lectin (PhoSL), three indoles are symmetrically arranged and form NH/π hydrogen bonds among each other. Here, we conducted quantum chemical calculations on this indole triad by using various methods and basis sets. The analyses revealed cooperativity in triad formation, with the many-body effect contributing approximately -2 kcal mol-1, which significantly stabilizes this protein. Symmetry-adapted perturbation theory ascribed this effect to the induced polarization. The electrostatic potential and atomic charges indeed revealed a charge redistribution through the NH/π hydrogen bond, which was favorable for triad formation.
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Affiliation(s)
- Kazuhiko Yamasaki
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Seiji Tsuzuki
- Department of Applied Physics, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-8656, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8566, Japan
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2
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Nochebuena J, Piquemal JP, Liu S, Cisneros GA. Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields. J Chem Theory Comput 2023; 19:7715-7730. [PMID: 37888874 DOI: 10.1021/acs.jctc.3c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Understanding cooperativity and frustration is crucial for studying biological processes such as molecular recognition and protein aggregation. Force fields have been extensively utilized to explore cooperativity in the formation of protein secondary structures and self-assembled systems. Multiple studies have demonstrated that polarizable force fields provide more accurate descriptions of this phenomenon compared to fixed-charge pairwise nonpolarizable force fields, thanks to the incorporation of polarization effects. In this study, we assess the performance of the AMOEBA polarizable force field and the AMBER and OPLS nonpolarizable pairwise force fields in capturing positive and negative cooperativity recently explored in neutral and charged molecular clusters using density functional theory. Our findings show that polarizable and nonpolarizable force fields qualitatively reproduce the relative cooperativity observed in electron structure calculations. However, AMBER and OPLS fail to describe absolute cooperativity. In contrast, AMOEBA accounts for the absolute cooperativity by considering interactions beyond pairwise interactions. According to the energy decomposition analysis, it is observed that the electrostatic interactions calculated with the AMBER and OPLS force fields seem to play an important and counterintuitive role in reproducing the adiabatic interaction energies calculated with density functional theory. However, it is important to note that these force fields, due to their nature, do not explicitly incorporate many-body effects, which limits their ability to accurately describe cooperativity. On the other hand, frustration in polarizable and nonpolarizable force fields is caused by changes in bond stretching and angle bending terms of the building blocks when they are forming a complex.
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Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jean-Philip Piquemal
- Laboratoire de Chimie théorique, Sorbonne Université, UMR 7616 CNRS, Paris 75005, France
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
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3
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Kondo HX, Nakamura H, Takano Y. Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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4
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Quantum chemical studies on hydrogen bonds in helical secondary structures. Biophys Rev 2023; 14:1369-1378. [PMID: 36659988 PMCID: PMC9842822 DOI: 10.1007/s12551-022-01034-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/30/2022] [Indexed: 01/07/2023] Open
Abstract
We present a brief review of our recent computational studies of hydrogen bonds (H-bonds) in helical secondary structures of proteins, α-helix and 310-helix, using a Negative Fragmentation Approach with density functional theory. We found that the depolarized electronic structures of the carbonyl oxygen of the ith residue and the amide hydrogen of the (i + 4)th residue cause weaker H-bond in an α-helix than in an isolated H-bond. Our calculations showed that the H-bond energies in the 310-helix were also weaker than those of the isolated H-bonds. In the 310-helices, the adjacent N-H group at the (i + 1)th residue was closer to the C=O group of the H-bond pair than the adjacent C=O group in the 310-helices, whereas the adjacent C=O group at the (i + 1)th residue was close to the H-bond acceptor in α-helices. Therefore, the destabilization of the H-bond is attributed to the depolarization caused by the adjacent residue of the helical backbone connecting the H-bond donor and acceptor. The differences in the change in electron density revealed that such depolarizations were caused by the local electronic interactions in their neighborhood inside the helical structure and redistributed the electron density. We also present the improvements in the force field of classical molecular simulation, based on our findings. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01034-5.
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Depolarizing Effects in Hydrogen Bond Energy in 3 10-Helices Revealed by Quantum Chemical Analysis. Int J Mol Sci 2022; 23:ijms23169032. [PMID: 36012292 PMCID: PMC9409261 DOI: 10.3390/ijms23169032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 12/18/2022] Open
Abstract
Hydrogen-bond (H-bond) energies in 310-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 310-helical conformation of total energies (whole helical model, WH3-10 model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH3-10 model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 310-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH3-10 model, suggesting the action of H-bond cooperativity.
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6
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Chen L, Li X, Xie Y, Liu N, Qin X, Chen X, Bu Y. Modulation of proton-coupled electron transfer reactions in lysine-containing alpha-helixes: alpha-helixes promoting long-range electron transfer. Phys Chem Chem Phys 2022; 24:14592-14602. [PMID: 35667661 DOI: 10.1039/d2cp00666a] [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
The proton-coupled electron transfer (PCET) reaction plays an important role in promoting many biological and chemical reactions. Usually, the rate of the PCET reaction increases with an increase in the electron transfer distance because long-range electron transfer requires more free energy barriers. Our density functional theory calculations here reveal that the mechanism of PCET occurring in lysine-containing alpha(α)-helixes changes with an increasing number of residues in the α-helical structure and the different conformations because of the modulation of the excess electron distribution by the α-helical structures. The rate constants of the corresponding PCET reactions are independent of or substantially shallower dependent on the electron transfer distances along α-helixes. This counter-intuitive behavior can be attributed to the fact that the formation of larger macro-cylindrical dipole moments in longer helixes can promote electron transfer along the α-helix with a low energy barrier. These findings may be useful to gain insights into long-range electron transfer in proteins and design α-helix-based electronics via the regulation of short-range proton transfer.
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Affiliation(s)
- Long Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Li
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxin Xie
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Nian Liu
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xin Qin
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Xiaohua Chen
- Chongqing Key Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, P. R. China.
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7
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Liu S, Rong C. Quantifying Frustrations for Molecular Complexes with Noncovalent Interactions. J Phys Chem A 2021; 125:4910-4917. [PMID: 34056899 DOI: 10.1021/acs.jpca.1c02690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular systems bound together through noncovalent interactions are involved in a lot of life-essential processes such as molecular recognition, signal transduction, and allosteric regulation. While cooperation as an important effect discovered in these systems focuses on the behavior of system's entirety, we need also examine the behavior of individual parts. In this work, using the distortion energy as the descriptor, we quantify frustration as the energetic loss of individual parts due to the formation of nonadditive molecular complexes. The applicability of our approach has been illustrated by a few simple clusters. Our results show that the frustration effect is smaller than the cooperation effect, but same as cooperativity, it can be both positive and negative. The ultimate benefit of a system made of multiple parts is dictated by the balance between the cooperative behavior among parts and the sacrifice from its individuals. This conflicting yet complementary conceptual pair of cooperation and frustration provides us with a different perspective from the systems' viewpoint for molecular complexes. This new angle of appreciating molecular complexes can be applied in conformational changes, enzymatic catalysis, and many more.
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Affiliation(s)
- Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States.,Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), and College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, P. R. China
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8
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Burdick DJ, Skelton NJ, Ultsch M, Beresini MH, Eigenbrot C, Li W, Zhang Y, Nguyen H, Kong-Beltran M, Quinn JG, Kirchhofer D. Design of Organo-Peptides As Bipartite PCSK9 Antagonists. ACS Chem Biol 2020; 15:425-436. [PMID: 31962046 DOI: 10.1021/acschembio.9b00899] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Proprotein convertase subtilisin/kexin 9 (PCSK9) has become an important therapeutic target for lipid lowering, since it regulates low-density lipoprotein cholesterol (LDL-c) levels by binding to liver LDL receptors (LDLR) and effecting their intracellular degradation. However, the development of small molecule inhibitors is hampered by the lack of attractive PCSK9 target sites. We recently discovered helical peptides that are able to bind to a cryptic groove site on PCSK9, which is situated in proximity to the main LDLR binding site. Here, we designed potent bipartite PCSK9 inhibitors by appending organic moieties to a helical groove-binding peptide to reach a hydrophobic pocket in the proximal LDLR binding region. The ultimately designed 1-amino-4-phenylcyclohexane-1-carbonyl extension improved the peptide affinity by >100-fold, yielding organo-peptide antagonists that potently inhibited PCSK9 binding to LDLR and preserved cellular LDLR. These new bipartite antagonists have reduced mass and improved potency compared to the first-generation peptide antagonists, further validating the PCSK9 groove as a viable therapeutic target site.
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9
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Canalp MB, Binder WH. Hybrid polymers bearing oligo-l-lysine(carboxybenzyl)s: synthesis and investigations of secondary structure. RSC Adv 2020; 10:1287-1295. [PMID: 35494681 PMCID: PMC9047569 DOI: 10.1039/c9ra09189k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/21/2019] [Indexed: 01/13/2023] Open
Abstract
Hybrid polymers of peptides resembling (partially) folded protein structures are promising materials in biomedicine, especially in view of folding-interactions between different segments. In this study polymers bearing repetitive peptidic folding elements, composed of N-terminus functionalized bis-ω-ene-functional oligo-l-lysine(carboxybenzyl(Z))s (Lysn) with repeating units (n) of 3, 6, 12, 24 and 30 were successfully synthesized to study their secondary structure introduced by conformational interactions between their chains. The pre-polymers of ADMET, narrowly dispersed Lysns, were obtained by ring opening polymerization (ROP) of N-carboxyanhydride (NCA) initiated with 11-amino-undecene, following N-terminus functionalization with 10-undecenoyl chloride. The resulting Lysns were subsequently polymerized via ADMET polymerization by using Grubbs’ first generation (G1) catalyst in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) generating the ADMET polymers (A-[Lysn]m) (m = 2–12) with molecular weights ranging from 3 to 28 kDa, displaying polydispersity (Đ) values in the range of 1.5–3.2. After chemical analyses of Lysns and A-[Lysn]ms by 1H-NMR, GPC and MALDI-ToF MS, secondary structural investigations were probed by CD spectroscopy and IR spectroscopy in 2,2,2-trifluoroethanol (TFE). In order to study A-[Lysn]ms with defined molecular weights and low polydispersity values (Đ = 1.03–1.48), the ADMET polymers A-[Lysn=3]m=3 and A-[Lysn=24]m=4 were fractionated by preparative GPC, and subsequently analysed by 1H-NMR, analytical GPC, MALDI-ToF MS and CD spectroscopy. We can demonstrate the influence of chain length of the generated polymers on the formation of secondary structures by comparing Lysns with varying n values to the ADMET-polymers with the help of spectroscopic techniques such as CD and FTIR-spectroscopy in a helicogenic solvent. We demonstrate the influence of chain length of segmented polymers bearing dynamic folding elements onto the formation of secondary structures with the help of spectroscopic techniques such as CD and FTIR-spectroscopy in a helicogenic solvent.![]()
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Affiliation(s)
- Merve Basak Canalp
- Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 Halle (Saale) D-06120 Germany
| | - Wolfgang H Binder
- Faculty of Natural Science II (Chemistry, Physics and Mathematics), Martin Luther University Halle-Wittenberg von-Danckelmann-Platz 4 Halle (Saale) D-06120 Germany
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10
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Bureau HR, Quirk S, Hernandez R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv 2020; 10:6520-6535. [PMID: 35495997 PMCID: PMC9049704 DOI: 10.1039/d0ra00920b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 11/21/2022] Open
Abstract
The single-point mutations of tprzip1 are indicated at left, and their relative energetics are compared at right.
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11
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Rong C, Zhao D, Zhou T, Liu S, Yu D, Liu S. Homogeneous Molecular Systems are Positively Cooperative, but Charged Molecular Systems are Negatively Cooperative. J Phys Chem Lett 2019; 10:1716-1721. [PMID: 30916572 DOI: 10.1021/acs.jpclett.9b00639] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Molecular systems bound together through noncovalent interactions are ubiquitous in nature, many of which are involved in essential life processes, yet little is known about the principles governing their structure, stability, and function. Cooperativity as one of the intrinsic properties in these systems plays a key role. In this work, on the basis of our recent quantification scheme of the cooperativity effect, we present a general pattern to identify which systems are positively cooperative and which are negatively cooperative. We show that cooperativity in homogeneous molecular systems is positive, but cooperativity in charged molecular systems is negative. We also employ analytical tools from energetics and information perspectives to appreciate the origin of the cooperativity effect. We find that positive cooperativity is dominated by the exchange-correlation interaction and steric effect, whereas negative cooperativity is governed by the electrostatic interaction. Our results should have strong implications for better understanding molecular recognition, protein folding, signal transduction, allosteric regulation, and other processes.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210093 , People's Republic of China
| | - Tianjing Zhou
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Siyuan Liu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Donghai Yu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha Hunan 410081 , People's Republic of China
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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12
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Jiang F, Wu HN, Kang W, Wu YD. Developments and Applications of Coil-Library-Based Residue-Specific Force Fields for Molecular Dynamics Simulations of Peptides and Proteins. J Chem Theory Comput 2019; 15:2761-2773. [DOI: 10.1021/acs.jctc.8b00794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hao-Nan Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Kang
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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13
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Liu L, Shi T, Houk KN, Zhao YL. Understanding the R882H mutation effects of DNA methyltransferase DNMT3A: a combination of molecular dynamics simulations and QM/MM calculations. RSC Adv 2019; 9:31425-31434. [PMID: 35527972 PMCID: PMC9072302 DOI: 10.1039/c9ra06791d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/15/2023] Open
Abstract
The AML-related high-frequent R882H mutation of DNA (cytosine-5)-methyltransferase 3A (DNMT3A), a key enzyme forde novoepigenetic methylation in human beings, was characterized by a disturbing conformation ofS-adenosylmethionine (SAM).
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Affiliation(s)
- Lanxuan Liu
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry
- University of California
- Los Angeles
- USA
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism
- Joint International Research Laboratory of Metabolic and Developmental Sciences
- School of Life Sciences and Biotechnology
- Shanghai Jiao Tong University
- Shanghai 200240
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14
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Rong C, Zhao D, Yu D, Liu S. Quantification and origin of cooperativity: insights from density functional reactivity theory. Phys Chem Chem Phys 2018; 20:17990-17998. [PMID: 29927447 DOI: 10.1039/c8cp03092h] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cooperativity is a widely used chemical concept whose existence is ubiquitous in chemical and biological systems but whose quantification is still controversial and origin much less appreciated. In this work, using the interaction energy of a molecular system, which is composed of multiple copies of a building block, we propose a quantitative measurement to evaluate the cooperativity effect. This quantification approach is then applied to six molecular systems, i.e., water cluster, argon cluster, protonated water cluster, zinc atom cluster, water cluster on top of a graphene sheet, and alpha helix of glycine amino acids, each with up to 20 copies of the building block. Cooperativity is seen in all these systems. Both positive and negative cooperativity effects are observed. Employing the two energy partition schemes in density functional theory and the information-theoretic quantities such as Shannon entropy, Fisher information, information gain, etc., we then examine the origin of the cooperativity effect for these systems. Strong linear correlations between the cooperativity measure and some of these theoretical quantities have been unveiled. With these correlations, we are able to quantitatively account for their origin of cooperativity. Our results show that the interactions governing the existence and validity of the cooperativity effect are complicated. An opposite mechanism in enthalpy-entropy compensation for positive and negative cooperativity has been unveiled. These results should provide new insights and understandings from a different viewpoint about the nature and origin of cooperativity to appreciate this vastly important chemical concept.
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Affiliation(s)
- Chunying Rong
- College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha Hunan 410081, P. R. China
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15
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Marklund EG, Zhang Y, Basha E, Benesch JLP, Vierling E. Structural and functional aspects of the interaction partners of the small heat-shock protein in Synechocystis. Cell Stress Chaperones 2018; 23:723-732. [PMID: 29476342 PMCID: PMC6045555 DOI: 10.1007/s12192-018-0884-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/09/2018] [Accepted: 02/01/2018] [Indexed: 01/28/2023] Open
Abstract
The canonical function of small heat-shock proteins (sHSPs) is to interact with proteins destabilized under conditions of cellular stress. While the breadth of interactions made by many sHSPs is well-known, there is currently little knowledge about what structural features of the interactors form the basis for their recognition. Here, we have identified 83 in vivo interactors of the sole sHSP in the cyanobacterium Synechocystis sp. PCC 6803, HSP16.6, reflective of stable associations with soluble proteins made under heat-shock conditions. By performing bioinformatic analyses on these interactors, we identify primary and secondary structural elements that are enriched relative to expectations from the cyanobacterial genome. In addition, by examining the Synechocystis interactors and comparing them with those identified to bind sHSPs in other prokaryotes, we show that sHSPs associate with specific proteins and biological processes. Our data are therefore consistent with a picture of sHSPs being broadly specific molecular chaperones that act to protect multiple cellular pathways.
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Affiliation(s)
- Erik G Marklund
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, 75123, Sweden
| | - Yichen Zhang
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
- Alorica, Inc., Irvine, CA, USA
| | - Eman Basha
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
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16
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Hu K, Jiang Y, Xiong W, Li H, Zhang PY, Yin F, Zhang Q, Geng H, Jiang F, Li Z, Wang X, Li Z. Tuning peptide self-assembly by an in-tether chiral center. SCIENCE ADVANCES 2018; 4:eaar5907. [PMID: 29756036 PMCID: PMC5947974 DOI: 10.1126/sciadv.aar5907] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/28/2018] [Indexed: 05/09/2023]
Abstract
The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.
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Affiliation(s)
- Kuan Hu
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing 100083, China
| | - Yixiang Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Xiong
- School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Hu Li
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Pei-Yu Zhang
- XtalPi Inc., One Broadway, 9th floor, Cambridge, MA 02142, USA
| | - Feng Yin
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Qianling Zhang
- Shenzhen Key Laboratory of Functional Polymer, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Hao Geng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Fan Jiang
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Zhou Li
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing 100083, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Xinwei Wang
- School of Advanced Materials, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
| | - Zigang Li
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Corresponding author. (Zigang L.); (X.W.); (Zhou L.); (F.J.)
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17
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Sun CL, Liu LP, Tian F, Ding F, Wang LW. Charge-patching method for the calculation of electronic structure of polypeptides. Phys Chem Chem Phys 2018; 20:23301-23310. [DOI: 10.1039/c8cp01803k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on the CPM method, the charge densities of polypeptides can be generated and their electronic structure can be further calculated.
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Affiliation(s)
- Chang-Liang Sun
- Center of Physical Chemistry Test
- Shenyang University of Chemical Technology
- Shenyang 110142
- People's Republic of China
- Materials Science Division
| | - Li-Ping Liu
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- School of Physics
| | - Fubo Tian
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- College of Physics
| | - Fu Ding
- Center of Physical Chemistry Test
- Shenyang University of Chemical Technology
- Shenyang 110142
- People's Republic of China
| | - Lin-Wang Wang
- Materials Science Division
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
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18
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Wu HN, Jiang F, Wu YD. Significantly Improved Protein Folding Thermodynamics Using a Dispersion-Corrected Water Model and a New Residue-Specific Force Field. J Phys Chem Lett 2017; 8:3199-3205. [PMID: 28651056 DOI: 10.1021/acs.jpclett.7b01213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature dependence of folding/unfolding equilibrium and overly collapsed unfolded or disordered states. For the latter problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage, and the GB1 hairpin). By using residue-specific parameters to achieve better match between amino acid sequences and native structures and adding a small H-bond correction to partially compensate the missing many-body effects in α-helix formation, the new RSFF2+ force field with the TIP4P-D water model can excellently reproduce experimental melting curves of both α-helical and β-hairpin systems. The RSFF2+/TIP4P-D method also gives less collapsed unfolded structures and describes well folded proteins simultaneously.
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Affiliation(s)
- Hao-Nan Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
| | - Yun-Dong Wu
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School , Shenzhen 518055, China
- College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China
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19
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Bottorf L, Rafferty S, Sahu ID, McCarrick RM, Lorigan GA. Utilizing Electron Spin Echo Envelope Modulation To Distinguish between the Local Secondary Structures of an α-Helix and an Amphipathic 3 10-Helical Peptide. J Phys Chem B 2017; 121:2961-2967. [PMID: 28339206 DOI: 10.1021/acs.jpcb.7b00626] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron spin echo envelope modulation (ESEEM) spectroscopy was used to distinguish between the local secondary structures of an α-helix and a 310-helix. Previously, we have shown that ESEEM spectroscopy in combination with site-directed spin labeling (SDSL) and 2H-labeled amino acids (i) can probe the local secondary structure of α-helices, resulting in an obvious deuterium modulation pattern, where i+4 positions generally show larger 2H ESEEM peak intensities than i+3 positions. Here, we have hypothesized that due to the unique turn periodicities of an α-helix (3.6 residues per turn with a pitch of 5.4 Å) and a 310-helix (3.1 residues per turn with a pitch of 5.8-6.0 Å), the opposite deuterium modulation pattern would be observed for a 310-helix. In this study, 2H-labeled d10-leucine (Leu) was substituted at a specific Leu residue (i) and a nitroxide spin label was positioned 2, 3, and 4 residues away (denoted i+2 to i+4) on an amphipathic model peptide, LRL8. When LRL8 is solubilized in trifluoroethanol (TFE), the peptide adopts an α-helical structure, and alternatively, forms a 310-helical secondary structure when incorporated into liposomes. Larger 2H ESEEM peaks in the FT frequency domain data were observed for the i+4 samples when compared to the i+3 samples for the α-helix whereas the opposite pattern was revealed for the 310-helix. These unique patterns provide pertinent local secondary structural information to distinguish between the α-helical and 310-helical structural motifs for the first time using this ESEEM spectroscopic approach with short data acquisition times (∼30 min) and small sample concentrations (∼100 μM) as well as providing more site-specific secondary structural information compared to other common biophysical approaches, such as CD.
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Affiliation(s)
- Lauren Bottorf
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Sophia Rafferty
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Robert M McCarrick
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
| | - Gary A Lorigan
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio 45056, United States
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20
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Li J, Lyu W, Rossetti G, Konijnenberg A, Natalello A, Ippoliti E, Orozco M, Sobott F, Grandori R, Carloni P. Proton Dynamics in Protein Mass Spectrometry. J Phys Chem Lett 2017; 8:1105-1112. [PMID: 28207277 DOI: 10.1021/acs.jpclett.7b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.
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Affiliation(s)
- Jinyu Li
- College of Chemistry, Fuzhou University , 350002 Fuzhou, China
| | - Wenping Lyu
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Faculty of Mathematics, Computer Science and Natural Sciences, RWTH-Aachen University , 52056 Aachen, Germany
- Computation-Based Science and Technology Research Center, Cyprus Institute , 2121 Aglantzia, Nicosia, Cyprus
| | - Giulia Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University , 52062 Aachen, Germany
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich , D-52425 Jülich, Germany
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Modesto Orozco
- Joint BSC-IRB Program on Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry group, Department of Chemistry, University of Antwerp , 2000 Antwerpen, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca , Piazza della Scienza 2, 20126 Milan, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- JARA-HPC, 52425 Jülich, Germany
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21
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Rapid prediction of interaction energies for nucleoside-containing hydrogen-bonded complexes: Lone-pair dipole moment treatment for adenine, cytosine and guanine. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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23
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Ireta J. Polyalanine α-helix microsolvation: assessing the energy of the peptide desolvation penalty with density functional theory. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1981-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Guo P, Lei X, Gao Y. Conformational flexibility of PPII-helix: A density functional theory study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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26
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Takano Y, Kusaka A, Nakamura H. Density functional study of molecular interactions in secondary structures of proteins. Biophys Physicobiol 2016; 13:27-35. [PMID: 27924255 PMCID: PMC5042169 DOI: 10.2142/biophysico.13.0_27] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/16/2016] [Indexed: 12/01/2022] Open
Abstract
Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.
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Affiliation(s)
- Yu Takano
- Institute for Protein Research, Osaka University
- Graduate School of Information Sciences, Hiroshima City University
- JST, CREST
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University
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27
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Li S, Li W, Ma J. Generalized energy-based fragmentation approach and its applications to macromolecules and molecular aggregates. Acc Chem Res 2014; 47:2712-20. [PMID: 24873495 DOI: 10.1021/ar500038z] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conspectus The generalized energy-based fragmentation (GEBF) approach provides a very simple way of approximately evaluating the ground-state energy or properties of a large system in terms of ground-state energies of various small "electrostatically embedded" subsystems, which can be calculated with any traditional ab initio quantum chemistry (X) method (X = Hartree-Fock, density functional theory, and so on). Due to its excellent parallel efficiency, the GEBF approach at the X theory level (GEBF-X) allows full quantum mechanical (QM) calculations to be accessible for systems with hundreds and even thousands of atoms on ordinary workstations. The implementation of the GEBF approach at various theoretical levels can be easily done with existing quantum chemistry programs. This Account reviews the methodology, implementation, and applications of the GEBF-X approach. This method has been successfully applied to optimize the structures of various large systems including molecular clusters, polypeptides, proteins, and foldamers. Such investigations could allow us to elucidate the origin and nature of the cooperative interaction in secondary structures of long peptides or the driving force of the self-assembly processes of aromatic oligoamides. These GEBF-based QM calculations reveal that the structures and stability of various complex systems result from a subtle balance of many types of noncovalent interactions such as hydrogen bonding and van der Waals interactions. The GEBF-based ab initio molecular dynamics (AIMD) method also allows the investigation of dynamic behaviors of large systems on the order of tens of picoseconds. It was demonstrated that the conformational dynamics of two model peptides predicted by GEBF-based AIMD are noticeably different from those predicted by the classical force field MD method. With the target of extending QM calculations to molecular aggregates in the condensed phase, we have implemented the GEBF-based multilayer hybrid models, which could provide satisfactory descriptions of the binding energies between a solute molecule and its surrounding waters and the chain-length dependence of the conformational changes of oligomers in aqueous solutions. A coarse-grained polarizable molecular mechanics model, furnished with GEBF-X dipole moments of subsystems, exhibits some advantages of treating the electrostatic polarization with reduced computational costs. We anticipate that the GEBF approach will continue to develop with the ultimate goal of studying complicated phenomena at mesoscopic scales and serve as a practical tool to elucidate the structure and dynamics of chemical and biological systems.
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Affiliation(s)
- Shuhua Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Wei Li
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical
Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute
of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People’s Republic of China
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28
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A B3LYP and MP2(full) theoretical investigation into cooperativity effects, aromaticity and thermodynamic properties in the Na(+)⋯benzonitrile⋯H2O ternary complex. J Mol Model 2014; 20:2341. [PMID: 25005001 DOI: 10.1007/s00894-014-2341-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 06/08/2014] [Indexed: 10/25/2022]
Abstract
The cooperativity effects between H-bonding and Na(+)⋯π or Na(+)⋯σ interactions in Na(+)⋯benzonitrile⋯H2O complexes were investigated using the B3LYP and MP2(full) methods with 6-311++G(2d,p) and aug-cc-pVTZ basis sets. The thermodynamic cooperativity and the influence of this cooperativity on aromaticity was evaluated by nucleus-independent chemical shifts (NICS). The results showed that the influence of the Na(+)⋯σ or Na(+)⋯π interaction on the hydrogen bond is more pronounced than that of the latter on the former. The cooperativity effect appeared in the Na(+)⋯σ interaction complex while the anti-cooperativity effect tended to be in the Na(+)⋯π system. The change in enthalpy is the major factor driving cooperativity. Thermodynamic cooperativity is not in accordance with the cooperativity effect evaluated by the change of interaction energy. The ring aromaticity of is weakened while the bond dissociation energy (BDE) of the C-CN bond increases upon ternary complex formation. The cooperativity effect (E coop) correlates with R c (NICS(1)ternary/NICS(1)binary) and ΔΔδ (Δδ ternary - Δδ binary) involving the ring and C ≡ N bond, as well as R BDE(C-CN) [BDE(C-CN)ternary/BDE(C-CN)binary], respectively. AIM (atoms in molecules) analysis confirms the existence of cooperativity.
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29
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A theoretical investigation into the cooperativity effect involving anionic hydrogen bond, thermodynamic property and aromaticity in Cl−⋯benzonitrile⋯H2O ternary complex. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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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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31
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Remya K, Suresh CH. Cooperativity and cluster growth patterns in acetonitrile: A DFT study. J Comput Chem 2014; 35:910-22. [DOI: 10.1002/jcc.23575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/22/2014] [Accepted: 02/04/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Karunakaran Remya
- Inorganic and Theoretical Chemistry Section, CSTD; CSIR-National Institute for interdisciplinary Science and Technology; Trivandrum 695 019 India
| | - Cherumuttathu H. Suresh
- Inorganic and Theoretical Chemistry Section, CSTD; CSIR-National Institute for interdisciplinary Science and Technology; Trivandrum 695 019 India
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32
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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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33
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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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34
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Alparone A. Evolution of Electric Dipole (Hyper)polarizabilities of β-Strand Polyglycine Single Chains: An ab Initio and DFT Theoretical Study. J Phys Chem A 2013; 117:5184-94. [DOI: 10.1021/jp403155q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrea Alparone
- Department of Chemistry, University of Catania, viale A. Doria 6, Catania -95125, Italy
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35
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Zhang M, Zhao J, Yang H, Liu P, Bu Y. 310-Helical Peptide Acting as a Dual Relay for Charge-Hopping Transfer in Proteins. J Phys Chem B 2013; 117:6385-93. [DOI: 10.1021/jp4012526] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Meng Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Jing Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Hongfang Yang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Ping Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
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36
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Rossi M, Scheffler M, Blum V. Impact of Vibrational Entropy on the Stability of Unsolvated Peptide Helices with Increasing Length. J Phys Chem B 2013; 117:5574-84. [DOI: 10.1021/jp402087e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Matthias Scheffler
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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37
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38
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Alparone A. The effect of secondary structures on the NLO properties of single chain oligopeptides: a comparison between β-strand and α-helix polyglycines. Phys Chem Chem Phys 2013; 15:12958-62. [DOI: 10.1039/c3cp51496j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Han B, Chen X, Zhao J, Bu Y. A peptide loop and an α-helix N-terminal serving as alternative electron hopping relays in proteins. Phys Chem Chem Phys 2012; 14:15849-59. [PMID: 23093308 DOI: 10.1039/c2cp41566f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This work presents a density functional theory calculational study for clarifying that peptide loops (-[peptide](n)-) including the N-terminal and the C-terminal oligopeptides and the α-helix N-terminal can serve as an intriguing kind of relay elements, as an addition to the known relay stations served by aromatic amino acids for electron hopping migration. For these protein motifs, an excess electron generally prefers to reside at the -NH(3)(+) group in a Rydberg state for the N-terminal peptides, or at the -COOH group in a dipole-bound state for the C-terminal peptides, and at the N-terminal in a dipole-bound π*-orbital state for the peptide loops and α-helices. The electron binding ability can be effectively enhanced by elongation for the α-helix N-terminal, and by bending, twisting, and even β-turning for the peptide chains. The relay property is determined by the local dipole instead of the total dipole of the peptide chains. Although no direct experiment supports this hypothesis, a series of recent studies regarding charge hopping migration associated with the peptide chains and helices could be viewed as strong evidence. But, further studies are still needed by considering the effects from relative redox potential between the donor and acceptor sites, protein environment, and structure water molecules.
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Affiliation(s)
- Boran Han
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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40
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 728] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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41
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Karjalainen EL, Ersmark T, Barth A. Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins. J Phys Chem B 2012; 116:4831-42. [DOI: 10.1021/jp301095v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eeva-Liisa Karjalainen
- Department of Biochemistry and Biophysics,
Arrhenius
Laboratories of Natural Sciences, Stockholm University, SE-106 91, Sweden
| | - Tore Ersmark
- Department of Biochemistry and Biophysics,
Arrhenius
Laboratories of Natural Sciences, Stockholm University, SE-106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics,
Arrhenius
Laboratories of Natural Sciences, Stockholm University, SE-106 91, Sweden
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42
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Le HA, Tan HJ, Ouyang JF, Bettens RPA. Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules. J Chem Theory Comput 2012; 8:469-78. [DOI: 10.1021/ct200783n] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Anh Le
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hwee-Jia Tan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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43
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Ionization energy and electron affinity of oligoglycines: a CAM-B3LYP density functional theory study. MONATSHEFTE FUR CHEMIE 2012. [DOI: 10.1007/s00706-011-0700-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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44
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Liu C, Zhao DX, Yang ZZ. Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system. J Comput Chem 2011; 33:379-90. [PMID: 22170234 DOI: 10.1002/jcc.21975] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 09/15/2011] [Accepted: 09/28/2011] [Indexed: 11/11/2022]
Abstract
The results of evaluating the individual hydrogen bond (H-bond) strength are expected to be helpful for the rational design of new strategies for molecular recognition or supramolecular assemblies. Unfortunately, there is few obvious and unambiguous means of evaluating the energy of a single H-bond within a multiple H-bonds system. We present a local analytic model, ABEEMσπ H-bond energy (HBE) model based on ab initio calculations (MP2) as benchmark, to directly and rapidly evaluate the individual HBE in situ in inter- and intramolecular multiple H-bonds system. This model describes the HBE as the sum of electrostatic and van der Waals (vdW) interactions which all depend upon the geometry and environment, and the ambient environment of H-bond in the model is accounted fairly. Thus, it can fairly consider the cooperative effect and secondary effect. The application range of ABEEMσπ HBE model is rather wide. This work has discussed the individual H-bond in DNA base pair and protein peptide dimers. The results indicate that the interactions among donor H atom, acceptor atom as well as those atoms connected to them with 1,2 or 1,3 relationships are all important for evaluating the HBE, although the interaction between the donor H atom and the acceptor atom is large. Furthermore, our model quantitatively indicates the polarization ability of N, O, and S in a new style, and gives the percentage of the polarization effect in HBE, which can not be given by fixed partial charge force field.
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Affiliation(s)
- Cui Liu
- Chemistry and Chemical Engineering Faculty, Liaoning Normal University, Dalian 116029, China
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45
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Gao Y, Lu X, Duan LL, Zhang JZH, Mei Y. Polarization of intraprotein hydrogen bond is critical to thermal stability of short helix. J Phys Chem B 2011; 116:549-54. [PMID: 22126129 DOI: 10.1021/jp208953x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Simulation result for protein folding/unfolding is highly dependent on the accuracy of the force field employed. Even for the simplest structure of protein such as a short helix, simulations using the existing force fields often fail to produce the correct structural/thermodynamic properties of the protein. Recent research indicated that lack of polarization is at least partially responsible for the failure to successfully fold a short helix. In this work, we develop a simple formula-based atomic charge polarization model for intraprotein (backbone) hydrogen bonding based on the existing AMBER force field to study the thermal stability of a short helix (2I9M) by replica exchange molecular dynamics simulation. By comparison of the simulation results with those obtained by employing the standard AMBER03 force field, the formula-based atomic charge polarization model gave the helix melting curve in close agreement with the NMR experiment. However, in simulations using the standard AMBER force field, the helix was thermally unstable at the temperature of the NMR experiment, with a melting temperature almost below the freezing point. The difference in observed thermal stability from these two simulations is the effect of backbone intraprotein polarization, which was included in the formula-based atomic charge polarization model. The polarization of backbone hydrogen bonding thus plays a critical role in the thermal stability of helix or more general protein structures.
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Affiliation(s)
- Ya Gao
- State Key Laboratory of Precision Spectroscopy and Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China
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46
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Haeffner F, Merle JK, Irikura KK. N-Protonated isomers as gateways to peptide ion fragmentation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:2222-2231. [PMID: 21952782 DOI: 10.1007/s13361-011-0241-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 08/23/2011] [Accepted: 08/24/2011] [Indexed: 05/31/2023]
Abstract
According to the popular "mobile proton model" for peptide ion fragmentation in tandem mass spectrometry, peptide bond cleavage is typically preceded by intramolecular proton transfer from basic sites to an amide nitrogen in the backbone. If the intrinsic barrier to dissociation is the same for all backbone sites, the fragmentation propensity at each amide bond should reflect the stability of the corresponding N-protonated isomer. This hypothesis was tested by using ab initio and force-field computations on several polyalanines and Leu-enkephalin. The results agree acceptably with experimental reports, supporting the hypothesis. It was found that backbone N-protonation is most favorable near the C-terminus. The preference for C-terminal N-protonation, which is stronger for longer polyalanines, may be understood in terms of the well known "helix macrodipole" in the corresponding helical conformations. The opposite stability trend is found for peptides constrained to be linear, which is initially surprising but turns out to be consistent with the reversed direction of the macrodipole in the linear conformation.
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Affiliation(s)
- Fredrik Haeffner
- Computational Chemistry Group, Chemical and Biochemical Reference Data Division, National Institute of Standards and Technology, Gaithersburg, MD 20899-8320, USA
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47
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Hua S, Xu L, Li W, Li S. Cooperativity in Long α- and 310-Helical Polyalanines: Both Electrostatic and van der Waals Interactions Are Essential. J Phys Chem B 2011; 115:11462-9. [DOI: 10.1021/jp203423w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Lina Xu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
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48
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Ismer L, Ireta J, Neugebauer J. A density functional theory based estimation of the anharmonic contributions to the free energy of a polypeptide helix. J Chem Phys 2011; 135:084122. [DOI: 10.1063/1.3629451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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49
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Zonta C, De Lucchi O, Motterle R, Serafini S. Cooperativity in benzotriazole-amine complexes: allosteric tuning of molecular recognition interfaces. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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50
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Mahadevi AS, Neela YI, Sastry GN. A theoretical study on structural, spectroscopic and energetic properties of acetamide clusters [CH3CONH2] (n = 1–15). Phys Chem Chem Phys 2011; 13:15211-20. [DOI: 10.1039/c1cp21346f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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