1
|
Zhao J, Dong T, Yu P, Wang J. Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2021; 126:161-173. [PMID: 34968072 DOI: 10.1021/acs.jpcb.1c10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na+, Ca2+, Mg2+, and Zn2+) with backbone (amide C═O) and C-terminal carboxylate (COO-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PPII) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH3+ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn2+) can specifically coordinate to the COO- group in bidentate and pseudo-bridging forms simultaneously. For Zn2+, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.
Collapse
Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| |
Collapse
|
2
|
Pan Z, Huang J, Zhuang W. Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study. JACS AU 2021; 1:1788-1797. [PMID: 34723281 PMCID: PMC8549111 DOI: 10.1021/jacsau.1c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.
Collapse
Affiliation(s)
- Zhijun Pan
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Shenzhen
Bay Laboratory, Guangming
District, Shenzhen 518107, China
| | - Jing Huang
- Westlake
Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural
Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Wei Zhuang
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy
of Sciences, Fuzhou, Fujian 35000, China
- Institute
of Urban Environment, Chinese Academy of
Sciences, XiaMen, Fujian 361021, China
| |
Collapse
|
3
|
Zhang Q, Pan Z, Zhang L, Zhang R, Chen Z, Jin T, Wu T, Chen X, Zhuang W. Ion effect on the dynamics of water hydrogen bonding network: A theoretical and computational spectroscopy point of view. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qiang Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
- Department of ChemistryBohai UniversityJinzhouChina
| | - Zhijun Pan
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Lu Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Ruiting Zhang
- School of Physics and Optoelectronic EngineeringXidian UniversityXi'anChina
| | - Zhening Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tan Jin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Tianmin Wu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Xian Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhouChina
| |
Collapse
|
4
|
Ju SW, Zhang N, Wang ZQ, Zhang RT, Zeng DW, Shao XP, Lin K. Contacted Ion Pairs in Aqueous CuCl2 by the Combination of Ratio Spectra, Difference Spectra, Second Order Difference Spectra in the UV-Visible Spectra. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1711211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Si-wen Ju
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Ning Zhang
- College of Science, Central South University of Forestry and Technology, Changsha 410004, China
| | - Zhi-qiang Wang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Rui-ting Zhang
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - De-wen Zeng
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Xiao-peng Shao
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| | - Ke Lin
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 710071, China
| |
Collapse
|
5
|
Yin Z, Inhester L, Thekku Veedu S, Quevedo W, Pietzsch A, Wernet P, Groenhof G, Föhlisch A, Grubmüller H, Techert S. Cationic and Anionic Impact on the Electronic Structure of Liquid Water. J Phys Chem Lett 2017; 8:3759-3764. [PMID: 28742347 DOI: 10.1021/acs.jpclett.7b01392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hydration shells around ions are crucial for many fundamental biological and chemical processes. Their local physicochemical properties are quite different from those of bulk water and hard to probe experimentally. We address this problem by combining soft X-ray spectroscopy using a liquid jet and molecular dynamics (MD) simulations together with ab initio electronic structure calculations to elucidate the water-ion interaction in a MgCl2 solution at the molecular level. Our results reveal that salt ions mainly affect the electronic properties of water molecules in close vicinity and that the oxygen K-edge X-ray emission spectrum of water molecules in the first solvation shell differs significantly from that of bulk water. Ion-specific effects are identified by fingerprint features in the water X-ray emission spectra. While Mg2+ ions cause a bathochromic shift of the water lone pair orbital, the 3p orbital of the Cl- ions causes an additional peak in the water emission spectrum at around 528 eV.
Collapse
Affiliation(s)
- Zhong Yin
- Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Ludger Inhester
- Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
- Center for Free-Electron Laser Science , Notkestrasse 85, 22607 Hamburg, Germany
| | - Sreevidya Thekku Veedu
- Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Wilson Quevedo
- Helmholtz-Zentrum Berlin GmbH , Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Annette Pietzsch
- Helmholtz-Zentrum Berlin GmbH , Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Philippe Wernet
- Helmholtz-Zentrum Berlin GmbH , Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Gerrit Groenhof
- University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä, Finland
| | - Alexander Föhlisch
- Helmholtz-Zentrum Berlin GmbH , Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- University of Potsdam , Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
| | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
- University of Göttingen , Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| |
Collapse
|
6
|
Terahertz echoes reveal the inhomogeneity of aqueous salt solutions. Nat Chem 2016; 9:273-278. [PMID: 28221356 DOI: 10.1038/nchem.2642] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/09/2016] [Indexed: 12/15/2022]
Abstract
The structural and dynamical properties of water are known to be affected by ion solvation. However, a consistent molecular picture that describes how and to what extent ions perturb the water structure is still missing. Here we apply 2D Raman-terahertz spectroscopy to investigate the impact of monatomic cations on the relaxation dynamics of the hydrogen-bond network in aqueous salt solutions. The inherent ability of multidimensional spectroscopy to deconvolute heterogeneous relaxation dynamics is used to reveal the correlation between the inhomogeneity of the collective intermolecular hydrogen-bond modes and the viscosity of a salt solution. Specifically, we demonstrate that the relaxation time along the echo direction t1 = t2 correlates with the capability of a given cation to 'structure' water. Moreover, we provide evidence that the echo originates from the water-water modes, and not the water-cation modes, which implies that cations can structure the hydrogen-bond network to a certain extent.
Collapse
|
7
|
Pan Z, Wu T, Jin T, Liu Y, Nagata Y, Zhang R, Zhuang W. Low frequency 2D Raman-THz spectroscopy of ionic solution: A simulation study. J Chem Phys 2015; 142:212419. [DOI: 10.1063/1.4917260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhijun Pan
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Tianmin Wu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Tan Jin
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yong Liu
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yuki Nagata
- Department for Molecular Spectroscopy, Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ruiting Zhang
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wei Zhuang
- State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| |
Collapse
|