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Krokidis MG, Exarchos TP, Avramouli A, Vrahatis AG, Vlamos P. Computational and Functional Insights of Protein Misfolding in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1423:201-206. [PMID: 37525045 DOI: 10.1007/978-3-031-31978-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Protein folding is the process by which a polypeptide chain self-assembles into the correct three-dimensional structure, so that it ends up in the biologically active, native state. Under conditions of proteotoxic stress, mutations, or cellular aging, proteins can begin to aggregate into non-native structures such as ordered amyloid fibrils and plaques. Many neurodegenerative diseases involve the misfolding and aggregation of specific proteins into abnormal, toxic species. Experimental approaches including crystallography and AFM (atomic force microscopy)-based force spectroscopy are used to exploit the folding and structural characterization of protein molecules. At the same time, computational techniques through molecular dynamics, fold recognition, and structure prediction are widely applied in this direction. Benchmarking analysis for combining and comparing computational methodologies with functional studies can decisively unravel robust interactions between the side groups of the amino acid sequence and monitor alterations in intrinsic protein dynamics with high precision as well as adequately determine potent conformations of the folded patterns formed in the polypeptide structure.
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Affiliation(s)
- Marios G Krokidis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece.
| | - Themis P Exarchos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Antigoni Avramouli
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Aristidis G Vrahatis
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
| | - Panagiotis Vlamos
- Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, Corfu, Greece
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Novelli F, Hoberg C, Adams EM, Klopf JM, Havenith M. Terahertz pump-probe of liquid water at 12.3 THz. Phys Chem Chem Phys 2021; 24:653-665. [PMID: 34570144 PMCID: PMC9096911 DOI: 10.1039/d1cp03207k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The dynamical complexity of the hydrogen-bonded water network can be investigated with intense Terahertz (THz) spectroscopy, which can drive the liquid into the nonlinear response regime and probe anharmonicity effects. Here we report single-color and polarization-dependent pump–probe experiments at 12.3 THz on liquid water, exciting the librational mode. By comparing results obtained on a static sample and a free-flowing water jet, we are able to disentangle the distinct contributions by thermal, acoustic, and nonlinear optical effects. We show that the transient transmission by the static water layer on a time scale of hundreds of microseconds can be described by thermal (slow) and acoustic (temperature-dependent) effects. In addition, during pump probe overlap we observe an anisotropic nonlinear optical response. This nonlinear signal is more prominent in the liquid jet than in the static cell, where temperature and density perturbations are more pronounced. Our measurements confirm that the THz excitation resonates with the rotationally-damped motion of water molecules, resulting in enhanced transient anisotropy. This model can be used to explain the non-linear response of water in the frequency range between about 1 and 20 THz. The excitation on the librational band of liquid water at 12.3 THz resonates with the rotationally-damped motion of water molecules.![]()
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Affiliation(s)
- Fabio Novelli
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany.
| | - Claudius Hoberg
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany.
| | - Ellen M Adams
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany.
| | - J Michael Klopf
- Institute of Radiation Physics, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany.
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Abstract
The solvation properties of liquid water originate from the transient network of hydrogen-bonded molecules. In order to probe the coupling between the different modes of this network, nonlinear terahertz (THz) spectroscopy techniques are required. Ideally, these techniques should use a minimal volume and capitalize on sensitive field-resolved detection. Here we performed open aperture z-scan transmission experiments on static liquid cells, and detect the THz fields with electro-optical techniques. We show that it is possible to quantify the nonlinear response of liquid water at ~1 THz even when large signals originate from the sample holder windows.
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Novelli F, Ruiz Pestana L, Bennett KC, Sebastiani F, Adams EM, Stavrias N, Ockelmann T, Colchero A, Hoberg C, Schwaab G, Head-Gordon T, Havenith M. Strong Anisotropy in Liquid Water upon Librational Excitation Using Terahertz Laser Fields. J Phys Chem B 2020; 124:4989-5001. [DOI: 10.1021/acs.jpcb.0c02448] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fabio Novelli
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Luis Ruiz Pestana
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Civil, Architectural, and Environmental Engineering, University of Miami, Coral Gables, Florida, United States
| | - Kochise C. Bennett
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Federico Sebastiani
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Ellen M. Adams
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Nikolas Stavrias
- Radboud University, FELIX Laboratory, Toernooiveld 7, Nijmegen, The Netherlands
| | - Thorsten Ockelmann
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Alejandro Colchero
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Claudius Hoberg
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Pitzer Center for Theoretical Chemistry, Departments of Chemistry, Chemical and Biomolecular Engineering, and Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
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Effect of aggregated Aβ protofilaments on intermolecular vibrational spectrum of confined water. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1699-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Leitner DM, Pandey HD, Reid KM. Energy Transport across Interfaces in Biomolecular Systems. J Phys Chem B 2019; 123:9507-9524. [DOI: 10.1021/acs.jpcb.9b07086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- David M. Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Hari Datt Pandey
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
| | - Korey M. Reid
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wirtz H, Schäfer S, Hoberg C, Reid KM, Leitner DM, Havenith M. Hydrophobic Collapse of Ubiquitin Generates Rapid Protein-Water Motions. Biochemistry 2018; 57:3650-3657. [PMID: 29790347 DOI: 10.1021/acs.biochem.8b00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report time-resolved measurements of the coupled protein-water modes of solvated ubiquitin during protein folding. Kinetic terahertz absorption (KITA) spectroscopy serves as a label-free technique for monitoring large scale conformational changes and folding of proteins subsequent to a sudden T-jump. We report here KITA measurements at an unprecedented time resolution of 500 ns, a resolution 2 orders of magnitude better than those of any previous KITA measurements, which reveal the coupled ubiquitin-solvent dynamics even in the initial phase of hydrophobic collapse. Complementary equilibrium experiments and molecular simulations of ubiquitin solutions are performed to clarify non-equilibrium contributions and reveal the molecular picture upon a change in structure, respectively. On the basis of our results, we propose that in the case of ubiquitin a rapid (<500 ns) initial phase of the hydrophobic collapse from the elongated protein to a molten globule structure precedes secondary structure formation. We find that these very first steps, including large-amplitude changes within the unfolded manifold, are accompanied by a rapid (<500 ns) pronounced change of the coupled protein-solvent response. The KITA response upon secondary structure formation exhibits an opposite sign, which indicates a distinct effect on the solvent-exposed surface.
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Affiliation(s)
- Hanna Wirtz
- Lehrstuhl für Physikalische Chemie II , Ruhr Universität Bochum , 44801 Bochum , Germany
| | - Sarah Schäfer
- Lehrstuhl für Physikalische Chemie II , Ruhr Universität Bochum , 44801 Bochum , Germany
| | - Claudius Hoberg
- Lehrstuhl für Physikalische Chemie II , Ruhr Universität Bochum , 44801 Bochum , Germany
| | - Korey M Reid
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - David M Leitner
- Department of Chemistry , University of Nevada , Reno , Nevada 89557 , United States
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II , Ruhr Universität Bochum , 44801 Bochum , Germany
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Wang J, Yuan C, Han Y, Wang Y, Liu X, Zhang S, Yan X. Trace Water as Prominent Factor to Induce Peptide Self-Assembly: Dynamic Evolution and Governing Interactions in Ionic Liquids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1702175. [PMID: 28976074 DOI: 10.1002/smll.201702175] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/12/2017] [Indexed: 05/22/2023]
Abstract
The interaction between water and biomolecules including peptides is of critical importance for forming high-level architectures and triggering life's functions. However, the bulk aqueous environment has limitations in detecting the kinetics and mechanisms of peptide self-assembly, especially relating to interactions of trace water. With ionic liquids (ILs) as a nonconventional medium, herein, it is discovered that trace amounts of water play a decisive role in triggering self-assembly of a biologically derived dipeptide. ILs provide a suitable nonaqueous environment, enabling us to mediate water content and follow the dynamic evolution of peptide self-assembly. The trace water is found to be involved in the assembly process of dipeptide, especially leading to the formation of stable noncovalent dipeptide oligomers in the early stage of nucleation, as evident by both experimental studies and theoretical simulations. The thermodynamics of the growth process is mainly governed by a synergistic effect of hydrophobic interaction and hydrogen bonds. Each step of assembly presents a different trend in thermodynamic energy. The dynamic evolution of assembly process can be efficiently mediated by changing trace water content. The decisive role of trace water in triggering and mediating self-assembly of biomolecules provides a new perspective in understanding supramolecular chemistry and molecular self-organization in biology.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yuchun Han
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Yilin Wang
- Key Laboratory of Colloid and Interface Science, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xiaomin Liu
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Suojiang Zhang
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Beijing Key Laboratory of Ionic Liquids Clean Process, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
- Center for Mesoscience, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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Pandey HD, Leitner DM. Thermodynamics of Hydration Water around an Antifreeze Protein: A Molecular Simulation Study. J Phys Chem B 2017; 121:9498-9507. [DOI: 10.1021/acs.jpcb.7b05892] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hari Datt Pandey
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
| | - David M. Leitner
- Department of Chemistry and
Chemical Physics Program, University of Nevada, Reno, Nevada 89557, United States
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11
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Novelli F, Chon JWM, Davis JA. Terahertz thermometry of gold nanospheres in water. OPTICS LETTERS 2016; 41:5801-5804. [PMID: 27973506 DOI: 10.1364/ol.41.005801] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The photo-thermal effects of plasmonic nanoparticles are promising for cancer therapies. These treatments would greatly benefit from real-time, multi-scale temperature mapping by non-invasive means. Here we show that intense terahertz time domain spectroscopy can be used as a non-contact and high-resolution thermometer of water solutions. Using this technique, we measure the temperature change, triggered by femtosecond amplified laser pulses, of a solution of gold nanospheres in water. Extensions of this ultra-fast and non-invasive technique could open the door to real-time micro-thermometry of single cells without fluorescent labels.
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Choi DH, Son H, Jeong JY, Park GS. Correlation between salt-induced change in water structure and lipid structure of multi-lamellar vesicles observed by terahertz time-domain spectroscopy. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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