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Yang X, Porcel E, Marichal L, Gonzalez-Vargas C, Khitous A, Salado-Leza D, Li X, Renault JP, Pin S, Remita H, Wien F, Lacombe S. Human Serum Albumin in the Presence of Small Platinum Nanoparticles. J Pharm Sci 2024; 113:1645-1652. [PMID: 38336007 DOI: 10.1016/j.xphs.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024]
Abstract
Noble metal materials, especially platinum nanoparticles (Pt NPs), have immense potential in nanomedicine as therapeutic agents on account of their high electron density and their high surface area. Intravenous injection is proposed as the best mode to deliver the product to patients. However, our understanding of the reaction of nanoparticles with blood components, especially proteins, is far behind the explosive development of these agents. Using synchrotron radiation circular dichroism (SRCD), we investigated the structural and stability changes of human serum albumin (HSA) upon interaction with PEG-OH coated Pt NPs at nanomolar concentrations, conditions potentially encountered for intravenous injection. There is no strong complexation found between HSA and Pt NPs. However, for the highest molar ratio of NP:HSA of 1:1, an increase of 18 °C in the thermal unfolding of HSA was observed, which is attributed to increased thermal stability of HSA generated by preferential hydration. This work proposes a new and fast method to probe the potential toxicity of nanoparticles intended for clinical use with intravenous injection.
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Affiliation(s)
- Xiaomin Yang
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Erika Porcel
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Laurent Marichal
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Cesar Gonzalez-Vargas
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Amine Khitous
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Daniela Salado-Leza
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France; CONAHCYT, Institute of Physics, Autonomous University of San Luis Potosi, 78295 San Luis Potosi, Mexico
| | - Xue Li
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | | | - Serge Pin
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Hynd Remita
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405 Orsay, France
| | - Frank Wien
- Synchrotron Soleil, 91190 Saint-Aubin, France.
| | - Sandrine Lacombe
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France.
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Cordinier A, Petukhov I, Hucher N, Grisel M. An Innovative Methodology to Characterize, at the Molecular Scale, Interactions in Polysaccharide Aqueous Solutions. Molecules 2024; 29:1787. [PMID: 38675607 PMCID: PMC11052356 DOI: 10.3390/molecules29081787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Characterizing molecular interactions at the microscopic level remains difficult and, therefore, represents a key target to better understand macromolecule and biomacromolecule behaviors in solution, alone, or in mixtures with others. Therefore, accurate characterization in liquid media, especially in aqueous solutions, without causing any perturbation of the system in which they are studied, is quite difficult. To this purpose, the present paper describes an innovative methodology based on fluorescence spectrophotometry. Two molecular fluorescent probes, namely 8-anilino-1-naphtalenesulfonic acid (ANS) and 2-benzofuryl-3-hydroxy-4(1H)-quinolone (3HQ-Bf), were selected to characterize, respectively, the dipole-dipole interactions and hydrophobic micro-domains, for the first one, and hydrogen bonding, for the second. As a support to study molecular interactions, xanthan, galactomannan, and corresponding mixtures of these substances which are well known to exhibit a synergy of interactions in well-defined mixture conditions were chosen. Once the methodology was set up, the existence of the three types of interactions in these systems was demonstrated, thus allowing the elucidation of the mechanisms of interactions at the molecular scale.
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Affiliation(s)
| | | | | | - Michel Grisel
- Université Le Havre Normandie, Normandie Univ, URCOM UR 3221, F-76600 Le Havre, France; (A.C.)
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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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Hall D, Basu G, Ito N. Computational biophysics and structural biology of proteins-a Special Issue in honor of Prof. Haruki Nakamura's 70th birthday. Biophys Rev 2023; 14:1211-1222. [PMID: 36620377 PMCID: PMC9809522 DOI: 10.1007/s12551-022-01039-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Receiving his initial training jointly in theoretical and applied physics at the University of Tokyo, Professor Haruki Nakamura has had a long and eventful scientific career, along the way helping to shape the way that biophysics is carried out in Japan. Concentrating his research efforts on the simulation of protein structure and function, he has, over his career arc, acted as director of the Institute for Protein Research (Osaka, Japan), director of the Protein Data Bank of Japan (PDBj), president of the Biophysical Society of Japan (BSJ), president of the Protein Science Society of Japan (PSSJ), and group leader and professor of Bioinformatics and Computational Structural Biology at Osaka University. In 2022, Prof. Haruki Nakamura turned 70 years old, and to mark this occasion, his scientific colleagues from around the world have combined their efforts to produce this Festschrift Issue of the IUPAB Biophysical Reviews journal around the theme of the computational biophysics and structural biology of proteins.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164 Japan
- Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Gautam Basu
- Department of Biophysics, Bose Institute, Centenary Campus, P-1/12 C.I.T. Scheme VII-M, Kolkata, 700054 India
| | - Nobutoshi Ito
- Medical Research Institute, Tokyo Medical and Dental University (TMDU), Yushima, Bunkyo-Ku, Tokyo, 113-8510 Japan
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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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The structure and properties of MFG-E8 and the In vitro assessment of its toxic effects on myoblast cells. Protein Expr Purif 2020; 178:105720. [PMID: 32771447 DOI: 10.1016/j.pep.2020.105720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/09/2020] [Accepted: 07/28/2020] [Indexed: 01/25/2023]
Abstract
Four high-molecular-weight protein fractions of milk fat globule membrane (MFGM) were isolated from bovine milk. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), MALDI-TOF/TOF™ and Liquid chromatography electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were used to measure the molecular sizes of the MFGM. Fourier transform infrared spectroscopy (FT-IR) and circular dichroism (CD) were performed to determine the conformations of the MFGM. The results showed that the main protein (98.33%) in MFGM protein fraction 2 was Milk fat globule epidermal growth factor-VIII (MFG-E8), with a molecular weight of 47.82 kDa. The secondary structural component measurements showed that the MFG-E8 consisted of 5% helix, 70% sheet and 25% random coil, and the results matched well with the prediction by SSPro 5.1 bioinformatic analysis. The thermograms analysis revealed that Td and△H of MFG-E8 were 60.50°Cand 132.29 kJ/mol. The in vitro digestibility of MFG-E8 showed that it can be enzymatically hydrolyzed in the stomach and relatively stable in the intestinal fluid. The in vitro C2C12 and Caco2 cell activity tests indicated that MFG-E8 promoted the proliferation of C2C12 myoblast cells without cytotoxicity. The biological functional properties of MFG-E8 may be related to the fact that MFG-E8 possesses a high level of β-sheet structure. Our results suggested that MFG-E8 possesses broad prospects not only for use in functional food products but also as a source of natural anti-sarcopenia drugs.
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Raskatov JA. A DFT study of structure and stability of pleated and rippled cross-β sheets with hydrophobic sidechains. Biopolymers 2020; 112:e23391. [PMID: 32737991 DOI: 10.1002/bip.23391] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/14/2020] [Accepted: 06/26/2020] [Indexed: 01/05/2023]
Abstract
The rippled cross-β sheet, a topography, in which mirror-image peptides are arranged with alternating chirality into a periodic two-dimensional network, is burgeoning as a new design principle for materials and biomedical applications. Experiments by the Schneider, Nilsson, and Raskatov labs have independently shown diverse racemic mixtures of aggregation-prone peptide of different sizes to favor the rippled over the pleated topography. Yet, systematic ab initio studies are lacking, and the field is yet to develop rules that would enable the design of new rippled cross-β frameworks from first principles. Here, DFT calculations were performed on a set of model systems, designed to begin understanding the impact that bulky, hydrophobic sidechains have upon the formation of pleated and rippled cross-β frameworks. It is hoped that this study will help stimulate the development of a predictive, general framework to enable rational design of rippled cross-β sheets in the future.
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Affiliation(s)
- Jevgenij A Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, USA
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9
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Kondo HX, Kusaka A, Kitakawa CK, Onari J, Yamanaka S, Nakamura H, Takano Y. Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J Comput Chem 2019; 40:2043-2052. [PMID: 31099907 PMCID: PMC6767508 DOI: 10.1002/jcc.25859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 11/24/2022]
Abstract
Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroko X. Kondo
- School of Regional Innovation and Social Design EngineeringFaculty of Engineering, Kitami Institute of Technology, 165 Koen‐choKitamiHokkaido090‐8507Japan
| | - Ayumi Kusaka
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
| | - Colin K. Kitakawa
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Jinta Onari
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Shusuke Yamanaka
- Graduate School of ScienceOsaka University, 1‐1 MachikaneyamachoToyonakaOsaka560‐0043Japan
| | - Haruki Nakamura
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
| | - Yu Takano
- Institute for Protein ResearchOsaka University, 3‐2 YamadaokaSuitaOsaka565‐0871Japan
- Graduate School of Information SciencesHiroshima City University, 3‐4‐1 Ozuka‐Higashi Asa‐Minami‐KuHiroshima731‐3194Japan
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10
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Han R, Rempfer K, Zhang M, Dobbek H, Zouni A, Dau H, Luber S. Investigating the Structure and Dynamics of Apo‐Photosystem II. ChemCatChem 2019. [DOI: 10.1002/cctc.201900351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruocheng Han
- Institut für ChemieUniversität Zürich Winterthurerstrasse 129 8057 Zürich Switzerland
| | - Katharina Rempfer
- Institut für ChemieUniversität Zürich Winterthurerstrasse 129 8057 Zürich Switzerland
| | - Miao Zhang
- Institut für BiologieHumboldt Universität zu Berlin Philippstrasse 13 10115 Berlin Germany
| | - Holger Dobbek
- Institut für BiologieHumboldt Universität zu Berlin Philippstrasse 13 10115 Berlin Germany
| | - Athina Zouni
- Institut für BiologieHumboldt Universität zu Berlin Philippstrasse 13 10115 Berlin Germany
| | - Holger Dau
- Institut für PhysikFreie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Sandra Luber
- Institut für ChemieUniversität Zürich Winterthurerstrasse 129 8057 Zürich Switzerland
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Kasahara K, Terazawa H, Takahashi T, Higo J. Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review. Comput Struct Biotechnol J 2019; 17:712-720. [PMID: 31303975 PMCID: PMC6603302 DOI: 10.1016/j.csbj.2019.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/29/2019] [Accepted: 06/11/2019] [Indexed: 11/19/2022] Open
Abstract
The molecular dynamics (MD) method is a promising approach toward elucidating the molecular mechanisms of intrinsically disordered regions (IDRs) of proteins and their fuzzy complexes. This mini-review introduces recent studies that apply MD simulations to investigate the molecular recognition of IDRs. Firstly, methodological issues by which MD simulations treat IDRs, such as developing force fields, treating periodic boundary conditions, and enhanced sampling approaches, are discussed. Then, several examples of the applications of MD to investigate molecular interactions of IDRs in terms of the two kinds of complex formations; coupled-folding and binding and fuzzy complex. MD simulations provide insight into the molecular mechanisms of these binding processes by sampling conformational ensembles of flexible IDRs. In particular, we focused on all-atom explicit-solvent MD simulations except for studies of higher-order assembly of IDRs. Recent advances in MD methods, and computational power make it possible to dissect the molecular details of realistic molecular systems involving the dynamic behavior of IDRs.
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Affiliation(s)
- Kota Kasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
- Corresponding author.
| | - Hiroki Terazawa
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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12
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Culka M, Galgonek J, Vymětal J, Vondrášek J, Rulíšek L. Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective. J Phys Chem B 2019; 123:1215-1227. [PMID: 30645123 DOI: 10.1021/acs.jpcb.8b09245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By combining bioinformatics with quantum-chemical calculations, we attempt to address quantitatively some of the physical principles underlying protein folding. The former allowed us to identify tripeptide sequences in existing protein three-dimensional structures with a strong preference for either helical or extended structure. The selected representatives of pro-helical and pro-extended sequences were converted into "isolated" tripeptides-capped at N- and C-termini-and these were subjected to an extensive conformational sampling and geometry optimization (typically thousands to tens of thousands of conformers for each tripeptide). For each conformer, the QM(DFT-D3)/COSMO-RS free-energy value was then calculated, Gconf(solv). The Δ Gconf(solv) is expected to provide an objective, unbiased, and quantitatively accurate measure of the conformational preference of the particular tripeptide sequence. It has been shown that irrespective of the helical vs extended preferences of the selected tripeptide sequences in context of the protein, most of the low-energy conformers of isolated tripeptides prefer the R-helical structure. Nevertheless, pro-helical tripeptides show slightly stronger helix preference than their pro-extended counterparts. Furthermore, when the sampling is repeated in the presence of a partner tripeptide to mimic the situation in a β-sheet, pro-extended tripeptides (exemplified by the VIV) show a larger free-energy benefit than pro-helical tripeptides (exemplified by the EAM). This effect is even more pronounced in a hydrophobic solvent, which mimics the less polar parts of a protein. This is in line with our bioinformatic results showing that the majority of pro-extended tripeptides are hydrophobic. The preference for a specific secondary structure by the studied tripeptides is thus governed by the plasticity to adopt to its environment. In addition, we show that most of the "naturally occurring" conformations of tripeptide sequences, i.e., those found in existing three-dimensional protein structures, are within ∼10 kcal·mol-1 from their global minima. In summary, our "ab initio" data suggest that complex protein structures may start to emerge already at the level of their small oligopeptidic units, which is in line with a hierarchical nature of protein folding.
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Affiliation(s)
- Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
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Matsui T, Yamamoto K, Fujita T, Morihashi K. Molecular Dynamics and Quantum Chemical Approach for the Estimation of an Intramolecular Hydrogen Bond Strength in Okadaic Acid. J Phys Chem B 2018; 122:7233-7242. [DOI: 10.1021/acs.jpcb.8b03272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Ogasawara N, Kasahara K, Iwai R, Takahashi T. Unfolding of α-helical 20-residue poly-glutamic acid analyzed by multiple runs of canonical molecular dynamics simulations. PeerJ 2018; 6:e4769. [PMID: 29780670 PMCID: PMC5958886 DOI: 10.7717/peerj.4769] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/24/2018] [Indexed: 11/20/2022] Open
Abstract
Elucidating the molecular mechanism of helix-coil transitions of short peptides is a long-standing conundrum in physical chemistry. Although the helix-coil transitions of poly-glutamic acid (PGA) have been extensively studied, the molecular details of its unfolding process still remain unclear. We performed all-atom canonical molecular dynamics simulations for a 20-residue PGA, over a total of 19 μs, in order to investigate its helix-unfolding processes in atomic resolution. Among the 28 simulations, starting with the α-helical conformation, all showed an unfolding process triggered by the unwinding of terminal residues, rather than by kinking and unwinding of the middle region of the chain. The helix-coil-helix conformation which is speculated by the previous experiments was not observed. Upon comparison between the N- and C-termini, the latter tended to be unstable and easily unfolded. While the probabilities of helix elongation were almost the same among the N-terminal, middle, and C-terminal regions of the chain, unwinding of the helix was enriched at the C-terminal region. The turn and 310-helix conformations were kinetic intermediates in the formation and deformation of α-helix, consistent with the previous computational studies for Ala-based peptides.
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Affiliation(s)
- Naoki Ogasawara
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Kota Kasahara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryosuke Iwai
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Takuya Takahashi
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
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15
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Lima Costa AH, Clemente WS, Bezerra KS, Lima Neto JX, Albuquerque EL, Fulco UL. Computational biochemical investigation of the binding energy interactions between an estrogen receptor and its agonists. NEW J CHEM 2018. [DOI: 10.1039/c8nj03521k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We present the energy profiles of estrogen receptor–agonist ligand interactions in atomic detail using a quantum biochemical approach.
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Affiliation(s)
- Aranthya H. Lima Costa
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Washington S. Clemente
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - Katyanna S. Bezerra
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | - José X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
| | | | - Umberto L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal-RN
- Brazil
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16
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Vinodha M, Senthilkumar K. Counter anion effect on structural, opto-electronic and charge transport properties of fused π-conjugated imidazolium compound. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1414965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. Vinodha
- Department of Physics, Bharathiar University, Coimbatore, India
| | - K. Senthilkumar
- Department of Physics, Bharathiar University, Coimbatore, India
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Harada R, Takano Y, Shigeta Y. Common folding processes of mini-proteins: Partial formations of secondary structures initiate the immediate protein folding. J Comput Chem 2017; 38:790-797. [DOI: 10.1002/jcc.24748] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/20/2016] [Accepted: 01/12/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
| | - Yu Takano
- Department of Biomedical Information Sciences; Graduate School of Information Sciences, Hiroshima City University; 3-4-1 Ozuka-Higashi, Asa-Minami-Ku Hiroshima 731-3194 Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba; 1-1-1 Tennodai Tsukuba Ibaraki 305-8577 Japan
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