1
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Penkov NV. Peculiarities of the Dynamical Hydration Shell of Native Conformation Protein Using a Bovine Serum Albumin Example. APPLIED SPECTROSCOPY 2024:37028241261097. [PMID: 38881287 DOI: 10.1177/00037028241261097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
This paper describes an approach based on the method of terahertz time-domain spectroscopy, which allows the analysis of dynamical hydration shells of proteins with a thickness of 1-2 nm. Using the example of bovine serum albumin in three conformations, it is shown that the hydration shells of the protein are characterized by increased binding of water molecules in the primary hydration layers, and in more distant areas of hydration, on the contrary, the water structure is somewhat destroyed. The fraction of free or weakly bound molecules, usually observed in the structure of liquid water in hydration shells, become more numerous but its average binding is greater than in undisturbed water. The energy distribution of hydrogen bonds in hydration shells is narrowed compared to undisturbed water. All these manifestations of hydration are most pronounced for the native conformation of the protein. Also, the hydration shells of the native protein are characterized by a smaller number of hydrogen bonds and a tendency to decrease their average energy compared to non-native conformations. The fact of a pronounced peculiarity of the hydration shells of the protein in the native conformation has been noted for different proteins before. However, the methodological approach used in this work for the first time allowed this peculiarity to be described by specific parameters of the intermolecular structure and dynamics of water.
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Affiliation(s)
- Nikita V Penkov
- Institute of Cell Biophysics, Federal Research Center, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
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2
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Linse JB, Hub JS. Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data. Commun Chem 2023; 6:272. [PMID: 38086909 PMCID: PMC10716392 DOI: 10.1038/s42004-023-01067-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 06/09/2024] Open
Abstract
Biological macromolecules in solution are surrounded by a hydration shell, whose structure differs from the structure of bulk solvent. While the importance of the hydration shell for numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a quantitative probe of the hydration shell structure has been missing. We show that small-angle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a protein-specific probe of the protein hydration shell that enables quantitative comparison with molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of protein force field and water model. By comparing computed Rg values from SAXS relative to SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort, we found that several but not all force fields yield a hydration shell contrast in remarkable agreement with experiments. The hydration shell contrast captured by Rg values depends strongly on protein charge and geometric shape, thus providing a protein-specific footprint of protein-water interactions and a novel observable for scrutinizing atomistic hydration shell models against experimental data.
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Affiliation(s)
- Johanna-Barbara Linse
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, 66123, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, 66123, Germany.
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3
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Pyne S, Pyne P, Mitra RK. The explicit role of interfacial hydration during polyethylene glycol induced lipid fusion: a THz spectroscopic investigation. Phys Chem Chem Phys 2023; 25:31326-31334. [PMID: 37960951 DOI: 10.1039/d3cp04868c] [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: 11/15/2023]
Abstract
While the phenomenon of excipient mediated membrane fusion has been studied widely, the inherent role of interfacial hydration involved in the process has mostly remained unaddressed. Here we report the experimental validation of the fact that PEG-induced membrane fusion is associated with the dehydration of the membrane(s). We explore the explicit hydration behavior at three different lipids (DOPC, POPC and DPPC) membranes with different aliphatic tails as they undergo fusogenic transition in the presence of PEG of average molecular weight of 4000 using THz-FTIR spectroscopy in the frequency window of 1.5-13.5 THz. Dynamic light scattering and electron microscopic measurements confirm the formation of different intermediate steps of the liposomes during the fusion process: bilayer aggregation, destabilization and finally lipid fusion. We observe that membrane hydration follows a systematic trend with the lipid specificity as the fusion process sets in.
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Affiliation(s)
- Sumana Pyne
- Department of Chemical and Biological Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
| | - Partha Pyne
- Department of Chemical and Biological Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
| | - Rajib Kumar Mitra
- Department of Chemical and Biological Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
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4
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Vural D, Shrestha UR, Petridis L, Smith JC. Water molecule ordering on the surface of an intrinsically disordered protein. Biophys J 2023; 122:4326-4335. [PMID: 37838830 PMCID: PMC10722392 DOI: 10.1016/j.bpj.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.
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Affiliation(s)
- Derya Vural
- Department of Physics, Marmara University, Istanbul, Türkiye; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
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5
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Penkov NV. Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules. Biophys Rev 2023; 15:833-849. [PMID: 37974994 PMCID: PMC10643733 DOI: 10.1007/s12551-023-01131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.
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Affiliation(s)
- Nikita V. Penkov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics RAS, 142290 Pushchino, Russia
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6
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Clark JA, Prabhu VM, Douglas JF. Molecular Dynamics Simulation of the Influence of Temperature and Salt on the Dynamic Hydration Layer in a Model Polyzwitterionic Polymer PAEDAPS. J Phys Chem B 2023; 127:8185-8198. [PMID: 37668318 PMCID: PMC10578162 DOI: 10.1021/acs.jpcb.3c03654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
We investigate the hydration of poly(3-[2-(acrylamido) ethyldimethylammonio] propanesulfonate) over a range of temperatures in pure water and with the inclusion of 0.1 mol/L NaCl using atomistic molecular dynamics simulation. Drawing on concepts drawn from the field of glass-forming liquids, we use the Debye-Waller parameter () for describing the water mobility gradient around the polybetaine backbone extending to an overall distance ≈18 Å. The water mobility in this layer is defined through the mean-square water molecule displacement at a time on the order of water's β-relaxation time. The brushlike topology of polybetaines leads to two regions in the dynamic hydration layer. The inner region of ≈10.5 Å is explored by pendant group conformational motions, and the outer region of ≈7.5 Å represents an extended layer of reduced water mobility relative to bulk water. The dynamic hydration layer extends far beyond the static hydration layer, adjacent to the polymer.
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Affiliation(s)
- Jennifer A. Clark
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Vivek M. Prabhu
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Jack F. Douglas
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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7
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Azizi K, Gori M, Morzan U, Hassanali A, Kurian P. Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution. PNAS NEXUS 2023; 2:pgad257. [PMID: 37575674 PMCID: PMC10416812 DOI: 10.1093/pnasnexus/pgad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023]
Abstract
The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.
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Affiliation(s)
- Khatereh Azizi
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Matteo Gori
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
| | - Uriel Morzan
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Ali Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Philip Kurian
- Quantum Biology Laboratory, Howard University, Washington, DC 20060, USA
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8
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Boob MM, Sukenik S, Gruebele M, Pogorelov TV. TMAO: Protecting proteins from feeling the heat. Biophys J 2023; 122:1414-1422. [PMID: 36916005 PMCID: PMC10111349 DOI: 10.1016/j.bpj.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/14/2023] [Accepted: 03/02/2023] [Indexed: 03/14/2023] Open
Abstract
Osmolytes are ubiquitous in the cell and play an important role in controlling protein stability under stress. The natural osmolyte trimethylamine N-oxide (TMAO) is used by marine animals to counteract the effect of pressure denaturation at large depths. The molecular mechanism of TMAO stabilization against pressure and urea denaturation has been extensively studied, but unlike the case of other osmolytes, the ability of TMAO to protect proteins from high temperature has not been quantified. To reveal the effect of TMAO on folded and unfolded protein ensembles and the hydration shell at different temperatures, we study a mutant of the well-characterized, fast-folding model protein B (PRB). We carried out, in total, >190 μs all-atom simulations of thermal folding/unfolding of PRB at multiple temperatures and concentrations of TMAO. The simulations show increased thermal stability of PRB in the presence of TMAO. Partly structured, compact ensembles are favored over the unfolded state. TMAO forms two shells near the protein: an outer shell away from the protein surface has altered H-bond lifetimes of water molecules and increases hydration of the protein to help stabilize it; a less-populated inner shell with an opposite TMAO orientation closer to the protein surface binds exclusively to basic side chains. The cooperative cosolute effect of the inner and outer shell TMAO has a small number of TMAO molecules "herding" water molecules into two hydration shells at or near the protein surface. The stabilizing effect of TMAO on our protein saturates at 1 M despite higher TMAO solubility, so there may be little evolutionary pressure for extremophiles to produce higher intracellular TMAO concentrations, if true in general.
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Affiliation(s)
- Mayank M Boob
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Shahar Sukenik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Taras V Pogorelov
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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9
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Saha R, Mitra RK. Trivalent cation-induced phase separation in proteins: ion specific contribution in hydration also counts. Phys Chem Chem Phys 2022; 24:23661-23668. [PMID: 36148614 DOI: 10.1039/d2cp01061e] [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
Multivalent (specifically trivalent) metal ions are known to induce microscopic phase separation (commonly termed as liquid-liquid phase separation (LLPS)) in negatively charged globular proteins even at ambient temperatures, the process being mostly driven by protein charge neutralization followed by aggregation. Recent simulation studies have revealed that such self-aggregation of proteins is entropy driven; however, it is associated with a solvation effect, which could as well be different from the usual notion of hydrophobic hydration. In this contribution we have experimentally probed the explicit change in hydration associated with ion-induced LLPS formation of a globular protein bovine serum albumin (BSA) at ambient temperature using FIR-THz FTIR spectroscopy (50-750 cm-1; 1.5-22.5 THz). We have used ions of different charges: Na+, K+, Ca2+, Mg2+, La3+, Y3+, Ho3+ and Al3+. We found that all the trivalent ions induce LLPS; the formation of large aggregates has been evidenced from dynamic light scattering (DLS) measurements, but without perturbing the protein structure as confirmed from circular dichroism (CD) measurements. From the frequency dependent absorption coefficient (α(ν)) measurements in the THz frequency domain we estimate the various stretching/vibrational modes of water and we found that ions, forming LLPS, produce definite perturbation in the overall hydration, the extent of which is ion specific, invoking the definite role of hydrophilic (electrostatic) hydration of ions in the observed LLPS process.
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Affiliation(s)
- Ria Saha
- Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD; Sector-III, Salt Lake, Kolkata-700106, India.
| | - Rajib Kumar Mitra
- Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD; Sector-III, Salt Lake, Kolkata-700106, India.
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10
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Qi P, Qian W, Guo L, Xue J, Zhang N, Wang Y, Zhang Z, Zhang Z, Lin L, Sun C, Zhu L, Liu W. Sensing with Femtosecond Laser Filamentation. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22187076. [PMID: 36146424 PMCID: PMC9504994 DOI: 10.3390/s22187076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 05/25/2023]
Abstract
Femtosecond laser filamentation is a unique nonlinear optical phenomenon when high-power ultrafast laser propagation in all transparent optical media. During filamentation in the atmosphere, the ultrastrong field of 1013-1014 W/cm2 with a large distance ranging from meter to kilometers can effectively ionize, break, and excite the molecules and fragments, resulting in characteristic fingerprint emissions, which provide a great opportunity for investigating strong-field molecules interaction in complicated environments, especially remote sensing. Additionally, the ultrastrong intensity inside the filament can damage almost all the detectors and ignite various intricate higher order nonlinear optical effects. These extreme physical conditions and complicated phenomena make the sensing and controlling of filamentation challenging. This paper mainly focuses on recent research advances in sensing with femtosecond laser filamentation, including fundamental physics, sensing and manipulating methods, typical filament-based sensing techniques and application scenarios, opportunities, and challenges toward the filament-based remote sensing under different complicated conditions.
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Affiliation(s)
- Pengfei Qi
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Wenqi Qian
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Lanjun Guo
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Jiayun Xue
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Nan Zhang
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Yuezheng Wang
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Zhi Zhang
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Tianjin 300350, China
| | - Zeliang Zhang
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
| | - Lie Lin
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Tianjin 300350, China
| | - Changlin Sun
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, Tianjin 300350, China
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
| | - Liguo Zhu
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900, China
| | - Weiwei Liu
- Institute of Modern Optics, Eye Institute, Nankai University, Tianjin 300350, China
- Tianjin Key Laboratory of Optoelectronic Sensor and Sensing Network Technology, Tianjin 300350, China
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11
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Pyne S, Pyne P, Mitra RK. Addition of cholesterol alters the hydration at the surface of model lipids: a spectroscopic investigation. Phys Chem Chem Phys 2022; 24:20381-20389. [PMID: 35983752 DOI: 10.1039/d2cp01905a] [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
Cholesterol is known to modify the phase behavior of model lipid membranes as it makes phospholipid bilayers more structured. Simulation results have shown that the addition of cholesterol allows more bulk-like water to protrude into phospholipid interfaces. However, such claims have not yet been verified experimentally. We have investigated the alteration in the hydrogen bond network structure of water at the surface of two model phospholipids DOPC and DOPG as cholesterol is added into these using ATR-FTIR spectroscopy in the FIR-THz region. Our measurements and analysis led us to probe the collective H-bond network explicitly at the lipid surface. A detailed principal component analysis of the measured data concludes that the water-water H-bond vibration dynamics gets slower at the lipid surface as compared to bulk water, the effect being more prominent in the case of the charged phospholipid, DOPG. However, as cholesterol is added and more bulk-like water protrudes into the liposome interface, the H-bond vibration gets weaker and correspondingly the dynamics gets accelerated.
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Affiliation(s)
- Sumana Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
| | - Partha Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
| | - Rajib Kumar Mitra
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
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12
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Pyne S, Pyne P, Kumar Mitra R. The inner hydration in surfactant/cholesterol vesicles differs from the outer one: a spectroscopic investigation. Chemphyschem 2022; 23:e202200337. [PMID: 35775165 DOI: 10.1002/cphc.202200337] [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: 05/20/2022] [Revised: 06/21/2022] [Indexed: 11/07/2022]
Abstract
Vesicles contain two aqueous regions: inner core and outer-to-bulk . It has remained an open question whether hydration behaviour in the inner core differs from the outer-to-bulk region, mostly owning to the inability of the conventional spectroscopic techniques to deconvolute the contribution from these two regions. We, using THz-FTIR spectroscopy (1.5-13.5 THz) experimentally probe the inner hydration of three differently charged surfactant/cholesterol vesicles composed of SDS, CTAB and Brij 30. Both dynamic light scattering (DLS) and atomic force microscopy (AFM) measurements affirm the transition from micelles to vesicles as cholesterol is added into surfactant solutions. FTIR measurements show that hydration behaviour changes significantly as micelles are converted into vesicles, the change been exclusively caused due to the formation of an inner core . Our measurements on the hydrogen bond stretch and librational motion of the inner hydration show distinct features compared to the overall hydration, which in turn is found to be surfactant type and cholesterol concentration dependent.
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Affiliation(s)
- Sumana Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Partha Pyne
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Rajib Kumar Mitra
- Department of Chemical Biological and Macromolecular Sciences, S N Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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13
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Santra S, Jana M. Influence of Aqueous Arginine Solution on Regulating Conformational Stability and Hydration Properties of the Secondary Structural Segments of a Protein at Elevated Temperatures: A Molecular Dynamics Study. J Phys Chem B 2022; 126:1462-1476. [PMID: 35147426 DOI: 10.1021/acs.jpcb.1c09583] [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
The effects of aqueous arginine solution on the conformational stability of the secondary structural segments of a globular protein, ubiquitin, and the structure and dynamics of the surrounding water and arginine were examined by performing atomistic molecular dynamics (MD) simulations. Attempts have been made to identify the osmolytic efficacy of arginine solution, and its influence in guiding the hydration properties of the protein at an elevated temperature of 450 K. The similar properties of the protein in pure water at elevated temperatures were computed and compared. Replica exchange MD simulation was performed to explore the arginine solution's sensitivity in stabilizing the protein conformations for a wide range of temperatures (300-450 K). It was observed that although all the helices and strands of the protein undergo unfolding at elevated temperature in pure water, they exhibited native-like conformational dynamics in the presence of arginine at both ambient and elevated temperatures. We find that the higher free energy barrier between the folded native and unfolded states of the protein primarily arises from the structural transformation of α-helix, relative to the strands. Our study revealed that the water structure around the secondary segments depends on the nature of amino acid compositions of the helices and strands. The reorientation of water dipoles around the helices and strands was found hindered due to the presence of arginine in the solution; such hindrance reduces the possibility of exchange of hydrogen bonds that formed between the secondary segments of protein and water (PW), and as a result, PW hydrogen bonds take longer time to relax than in pure water. On the other hand, the origin of slow relaxation of protein-arginine (PA) hydrogen bonds was identified to be due to the presence of different types of protein-bound arginine molecules, where arginine interacts with the secondary structural segments of the protein through multiple/bifurcated hydrogen bonds. These protein-bound arginine formed different kinds of bridged PA hydrogen bonds between amino acid residues of the same secondary segments or among multiple bonds and helped protein to conserve its native folded form firmly.
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Affiliation(s)
- Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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Pyne P, Das Mahanta D, Gohil H, Prabhu SS, Mitra RK. Correlating solvation with conformational pathways of proteins in alcohol-water mixtures: a THz spectroscopic insight. Phys Chem Chem Phys 2021; 23:17536-17544. [PMID: 34369530 DOI: 10.1039/d1cp01841h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water, being an active participant in most of the biophysical processes, is important to trace how protein solvation changes as its conformation evolves in the presence of solutes or co-solvents. In this study, we investigate how the secondary structures of two diverse proteins - lysozyme and β-lactoglobulin - change in the aqueous mixtures of two alcohols - ethanol and 2,2,2-trifluoroethanol (TFE) using circular dichroism measurements. We observe that these alcohols change the secondary structures of these proteins and the changes are protein-specific. Subsequently, we measure the collective solvation dynamics of these two proteins both in the absence and in the presence of alcohols by measuring the frequency-dependent absorption coefficient (α(ν)) in the THz (0.1-1.2 THz) frequency domain. The alcohol-water mixtures exhibit a non-ideal behaviour with the highest absorption difference (Δα) obtained at Xalcohol = 0.2. The protein solvation in the presence of the alcohols shows an oscillating behaviour in which Δαprotein changes with Xalcohol. Such an oscillatory behaviour of protein solvation results from a delicate interplay between the protein-water, protein-alcohol and water-alcohol associations. We attempt to correlate the various structural conformations of the proteins with the associated solvation.
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Affiliation(s)
- Partha Pyne
- Department of Chemical, Biological & Macromolecular Sciences, S.N. Bose National Centre for Basic Sciences, Block-JD; Sector-III; Salt Lake, Kolkata-700106, India.
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15
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16
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Tokunaga Y, Tanaka M, Iida H, Kinoshita M, Tojima Y, Takeuchi K, Imashimizu M. Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin. Biophys J 2021; 120:2386-2393. [PMID: 33894216 PMCID: PMC8390810 DOI: 10.1016/j.bpj.2021.04.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/23/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 310 helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.
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Affiliation(s)
- Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hitoshi Iida
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Moto Kinoshita
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yuya Tojima
- Research Institute for Physical Measurement, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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Penkov NV, Penkova N. Key Differences of the Hydrate Shell Structures of ATP and Mg·ATP Revealed by Terahertz Time-Domain Spectroscopy and Dynamic Light Scattering. J Phys Chem B 2021; 125:4375-4382. [PMID: 33882673 DOI: 10.1021/acs.jpcb.1c02276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ATP is one of the main biological molecules. Many of its biological and physicochemical properties, such as energy capacity of the phosphate bonds, significantly depend on hydration. However, the structure of the hydration shell of the ATP molecule is still a matter of discussion. In this work, the hydration shells of ATP in water and MgCl2 solutions were examined by terahertz time-domain spectroscopy and dynamic light scattering. Terahertz spectroscopy reveals the distorted water structure in the ATP water solution displaying tightly bound water molecules, which could be explained by the hydration of phosphate groups. Upon ATP binding to a Mg2+ ion, the situation is principally different: Instead of the distorted water structure, its arranged structure with increased hydrogen bond number is observed. Dynamic light scattering showed that the hydrodynamic diameter of ATP increases by 0.5 nm after Mg2+ binding. Meanwhile, according the characteristics of scattering, the increase of the shell size occurs via formation of a layer with a refraction coefficient similar to water. This layer can be interpreted as hydration shell differing from unaltered water by increased number of hydrogen bonds.
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Affiliation(s)
- Nikita V Penkov
- Institute of Cell Biophysics RAS, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino 142290, Russia
| | - Nadezda Penkova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Russia
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18
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Tang M, Zhang M, Xia L, Wei D, Yang Z, Yan S, Du C, Cui HL. Detection of gene mutation responsible for Huntington's disease by terahertz attenuated total reflection microfluidic spectroscopy. JOURNAL OF BIOPHOTONICS 2021; 14:e202000315. [PMID: 32981137 DOI: 10.1002/jbio.202000315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Terahertz absorption spectroscopy based on attenuated total reflection (ATR) from a microfluidic sample cell was designed and implemented to detect gene mutations leading to Huntington's disease (HD). The self-developed compact ATR microfluidic system was employed to detect two groups of base-repeated DNA molecules combined with a terahertz time-domain spectrometer in a marker-free manner. The first group featured different repetition patterns of oligonucleotide fragments, and the second group included the HD gene. For the oligonucleotides of different repetition patterns, there were significant differences among the three oligonucleotides with three repeats of the double bases, which could be unambiguously classified and identified; For the HD gene, it was found that the magnitude of the terahertz absorption coefficients of the four oligonucleotide solutions was, in ascending order, CAG-4 < CAG-16 < CAG-32 < CAG-40 (the numbers are the repeat times of the CAG base segment, with 40 repeats belonging to the HD gene), when the concentration of oligonucleotide was 1 mg/mL. Principal component analysis result indicated that the spectral differences of the four oligonucleotide solutions with different CAG repeat times were statistically significant and clearly distinguishable. These results demonstrate the potential of terahertz spectroscopy as a noninvasive, unmarked, fast and low-cost assay for gene diagnosis and clinical disease detection.
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Affiliation(s)
- Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingkun Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Liangping Xia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- Key Laboratory of Micro Nano Optoelectronic Devices and Intelligent Perception Systems, Yangtze Normal University, Chongqing, China
| | - Dongshan Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
- School of Electronic Engineering, Dongguan University of Technology, Dongguan, China
| | - Zhongbo Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Chunlei Du
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Hong-Liang Cui
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
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Tang M, Zhang M, Xia L, Yang Z, Yan S, Wang H, Wei D, Du C, Cui HL. Detection of single-base mutation of DNA oligonucleotides with different lengths by terahertz attenuated total reflection microfluidic cell. BIOMEDICAL OPTICS EXPRESS 2020; 11:5362-5372. [PMID: 33014620 PMCID: PMC7510857 DOI: 10.1364/boe.400487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 05/15/2023]
Abstract
Many human genetic diseases are caused by single-base mutation in the gene sequence. Since DNA molecules with single-base mutation are extremely difficult to differentiate, existing detection methods are invariably complex and time-consuming. We propose a new label-free and fast terahertz (THz) spectroscopic technique based on a home-made terahertz attenuated total reflection (ATR) microfluidic cell and a terahertz time-domain spectroscopy (THz-TDS) system to detect single-base-mutated DNA molecules. The detected object DNA molecules are normal hemoglobin gene, sickle cell anemia gene (15 nt), JAK2 gene wild type and JAK2 V617F gene mutation (39 nt) from sickle cell anemia and thrombocytopenia, respectively. Results show that the oligonucleotide fragments with single-base mutation can be identified by THz spectroscopy combined with the ATR microfluidic cell, and the recognition effect of short oligonucleotide fragments with single-base mutation is better than that of long oligonucleotide fragments. The terahertz biosensor is shown to have high sensitivity and can be used to detect DNA molecules directly in the solution environment.
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Affiliation(s)
- Mingjie Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- These authors contributed equally to this work
| | - Mingkun Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- These authors contributed equally to this work
| | - Liangping Xia
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- Key Laboratory of Micro Nano Optoelectronic Devices and Intelligent Perception Systems, Yangtze Normal University, Chongqing, 408100, China
| | - Zhongbo Yang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shihan Yan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Huabin Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Dongshan Wei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
- School of Electronic Engineering, Dongguan University of Technology, Dongguan, Guangdong, 523808, China
| | - Chunlei Du
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
| | - Hong-Liang Cui
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China
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20
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Schewa S, Schroer MA, Zickmantel T, Song YH, Blanchet CE, Gruzinov AY, Katona G, Svergun DI, Roessle M. A THz transparent 3D printed microfluidic cell for small angle x-ray scattering. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:084101. [PMID: 32872894 DOI: 10.1063/5.0004706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle x-ray scattering (SAXS) is a powerful method to study the structure and domain movements of proteins in solution. Here, we present a microfluidic cell for SAXS experiments, which is also transparent for THz radiation. Specifically, cell dimensions and material were optimized for both radiation sources. In addition, the polystyrene cell can be 3D printed and easily assembled. We demonstrate the practicality of our design for SAXS measurements on several proteins in solution.
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Affiliation(s)
- S Schewa
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
| | - M A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Zickmantel
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Y-H Song
- Physics Institute, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - C E Blanchet
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - A Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - G Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - D I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - M Roessle
- University of Applied Sciences Lübeck, Mönkhofer Weg 239, 23562 Lübeck, Germany
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21
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Nemova EF, Cherkasova OP, Nikolaev NA, Dultseva GG. A Study on Molecular Mechanisms of Terahertz Radiation Interaction with Biopolymers Based on the Example of Bovine Serum Albumin. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s000635092003015x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Effect of aggregation on hydration of HSA protein: Steady-state Terahertz absorption spectroscopic study. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1696-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Alfarano SR, Vondracek H, Sebastiani F, Novelli F, Hoberg C, Kolling I, Brubach JB, Roy P, Schwaab G, Havenith M. Does hydrated glycine act as solidification nucleus at multi-kilobar conditions? Biophys Chem 2019; 253:106215. [DOI: 10.1016/j.bpc.2019.106215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/29/2019] [Accepted: 06/29/2019] [Indexed: 11/16/2022]
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24
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Das Mahanta D, Islam SI, Choudhury S, Das DK, Mitra RK, Barman A. Contrasting hydration dynamics in DME and DMSO aqueous solutions: A combined optical pump-probe and GHz-THz dielectric relaxation investigation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Morales-Hernández JA, Singh AK, Villanueva-Rodriguez SJ, Castro-Camus E. Hydration shells of carbohydrate polymers studied by calorimetry and terahertz spectroscopy. Food Chem 2019; 291:94-100. [DOI: 10.1016/j.foodchem.2019.03.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 11/15/2022]
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26
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Marques MPM, Batista de Carvalho ALM, Mamede AP, Santos IP, García Sakai V, Dopplapudi A, Cinque G, Wolna M, Gardner P, Batista de Carvalho LAE. Chemotherapeutic Targets in Osteosarcoma: Insights from Synchrotron-MicroFTIR and Quasi-Elastic Neutron Scattering. J Phys Chem B 2019; 123:6968-6979. [PMID: 31339317 DOI: 10.1021/acs.jpcb.9b05596] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This study aimed at the development of improved drugs against human osteosarcoma, which is the most common primary bone tumor in children and teenagers with a low prognosis. New insights into the impact of an unconventional Pd(II) anticancer agent on human osteosarcoma cells were obtained by synchrotron radiation-Fourier transform infrared microspectroscopy and quasi-elastic neutron scattering (QENS) experiments from its effect on the cellular metabolism to its influence on intracellular water, which can be regarded as a potential secondary pharmacological target. Specific infrared biomarkers of drug action were identified, enabling a molecular-level description of variations in cellular biochemistry upon drug exposure. The main changes were detected in the protein and lipid cellular components, namely, in the ratio of unsaturated-to-saturated fatty acids. QENS revealed reduced water mobility within the cytoplasm for drug-treated cells, coupled to a disruption of the hydration layers of biomolecules. Additionally, the chemical and dynamical profiles of osteosarcoma cells were compared to those of metastatic breast cancer cells, revealing distinct dissimilarities that may influence drug activity.
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Affiliation(s)
- Maria Paula M Marques
- "Química-Física Molecular", Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal.,Department of Life Sciences , University of Coimbra , 3000-456 Coimbra , Portugal
| | | | - Adriana P Mamede
- "Química-Física Molecular", Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Inês P Santos
- "Química-Física Molecular", Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Victoria García Sakai
- ISIS Facility , STFC Rutherford Appleton Laboratory , Chilton, Didcot , Oxfordshire OX11 0QX , U.K
| | - Asha Dopplapudi
- ISIS Facility , STFC Rutherford Appleton Laboratory , Chilton, Didcot , Oxfordshire OX11 0QX , U.K
| | - Gianfelice Cinque
- Diamond Light Source , Harwell Science and Innovation Campus , Chilton, Didcot , Oxfordshire OX11 0DE , U.K
| | - Magda Wolna
- Diamond Light Source , Harwell Science and Innovation Campus , Chilton, Didcot , Oxfordshire OX11 0DE , U.K
| | - Peter Gardner
- Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , U.K
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Wang P, Wang X, Liu L, Zhao H, Qi W, He M. The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy. Biophys J 2019; 117:533-541. [PMID: 31326108 DOI: 10.1016/j.bpj.2019.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 06/04/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is believed to be a significant biological mechanism related to neurodegenerative disease, which makes the early-stage detection of aggregates a major concern. We demonstrated the use of terahertz (THz) time-domain spectroscopy to study protein-water interaction of monomeric and dimeric bovine insulin in aqueous samples. Regulated by changing pH and verified by size-exclusion chromatography and dynamic light scattering, we then measured their concentration-dependent changes in THz absorption between 0.5 and 3.0 THz and quantitatively deduced the extended hydration shell thickness by cubic distribution model and random distribution model. Under a random distribution assumption, the extended hydration thickness is 15.4 ± 0.4 Å for monomeric insulin and 17.5 ± 0.5 Å for dimeric insulin, with the hydration number of 6700 and 11,000, respectively. The hydration number of dimeric insulin is not twice but 1.64 times that of monomeric insulin, further supported by the ratio of solvent-accessible surface area. This "1.64-times" relation probably originates from the structural and conformational changes accompanied with dimerization. Combined with the investigations on insulin samples with different single amino acid mutations, residue B24 is believed to play an important role in the dimerization process. It is demonstrated that THz time-domain spectroscopy is a useful tool and has the sensitivity to provide the hydration information of different protein aggregates at an early stage.
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Affiliation(s)
- Pengfei Wang
- State Key Laboratory of Precision Measuring Technology and Instruments
| | | | - Liyuan Liu
- Key Laboratory of Optoelectronic Information Technology, Ministry of Education of China, Tianjin University, Tianjin, People's Republic of China
| | - Hongwei Zhao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering
| | - Mingxia He
- State Key Laboratory of Precision Measuring Technology and Instruments.
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29
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Sasaki K, Popov I, Feldman Y. Water in the hydrated protein powders: Dynamic and structure. J Chem Phys 2019; 150:204504. [DOI: 10.1063/1.5096881] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Kaito Sasaki
- Micro/Nano Technology Center, Tokai University, 4-1-1 Kitakaname, Hiratsuka-shi, Kanagawa, Japan
- Department of Applied Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
| | - Ivan Popov
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yuri Feldman
- Department of Applied Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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30
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Danciu M, Alexa-Stratulat T, Stefanescu C, Dodi G, Tamba BI, Mihai CT, Stanciu GD, Luca A, Spiridon IA, Ungureanu LB, Ianole V, Ciortescu I, Mihai C, Stefanescu G, Chirilă I, Ciobanu R, Drug VL. Terahertz Spectroscopy and Imaging: A Cutting-Edge Method for Diagnosing Digestive Cancers. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E1519. [PMID: 31075912 PMCID: PMC6539301 DOI: 10.3390/ma12091519] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/05/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
The Terahertz's wavelength is located between the microwave and the infrared region of the electromagnetic spectrum. Because it is non-ionizing and non-invasive, Terahertz (THz)-based detection represents a very attractive tool for repeated assessments, patient monitoring, and follow-up. Cancer acts as the second leading cause of death in many regions, and current predictions estimate a continuous increasing trend. Of all types of tumors, digestive cancers represent an important percentage and their incidence is expected to increase more rapidly than other tumor types due to unhealthy lifestyle habits. Because it can precisely differentiate between different types of molecules, depending on water content, the information obtained through THz-based scanning could have several uses in the management of cancer patients and, more importantly, in the early detection of different solid tumors. The purpose of this manuscript is to offer a comprehensive overview of current data available on THz-based detection for digestive cancers. It summarizes the characteristics of THz waves and their interaction with tissues and subsequently presents available THz-based technologies (THz spectroscopy, THz-tomography, and THZ-endoscope) and their potential for future clinical use. The third part of the review is focused on highlighting current in vitro and in vivo research progress in the field, for identifying specific digestive cancers known as oral, esophageal, gastric, colonic, hepatic, and pancreatic tumors.
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Affiliation(s)
- Mihai Danciu
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Teodora Alexa-Stratulat
- Medical Oncology-Radiotherapy, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Cipriana Stefanescu
- Department of Biophysics and Medical Physics-Nuclear Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gianina Dodi
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Bogdan Ionel Tamba
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Cosmin Teodor Mihai
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gabriela Dumitrita Stanciu
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Andrei Luca
- Advanced Research and Development Center for Experimental Medicine (CEMEX), Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Irene Alexandra Spiridon
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | | | - Victor Ianole
- Pathology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Irina Ciortescu
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Catalina Mihai
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Gabriela Stefanescu
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Ioan Chirilă
- Environmental Health, National Institute of Public Health, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
| | - Romeo Ciobanu
- Electrical Engineering Faculty, Gheorghe Asachi Technical University of Iasi, 700050 Iasi, Romania.
| | - Vasile Liviu Drug
- Gastroenterology Department, Grigore T. Popa University of Medicine and Pharmacy of Iasi, 700051 Iasi, Romania.
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31
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Combarro Palacios I, Olsson C, Kamma-Lorger CS, Swenson J, Cerveny S. Motions of water and solutes-Slaving versus plasticization phenomena. J Chem Phys 2019; 150:124902. [PMID: 30927900 DOI: 10.1063/1.5030064] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It is well-accepted that hydration water is crucial for the structure, dynamics, and function of proteins. However, the exact role of water for the motions and functions of proteins is still debated. Experiments have shown that protein and water dynamics are strongly coupled but with water motions occurring on a considerably faster time scale (the so-called slaving behavior). On the other hand, water also reduces the conformational entropy of proteins and thereby acts as a plasticizer of them. In this work, we analyze the dynamics (using broadband dielectric spectroscopy) of some specific non-biological water solutions in a broad concentration range to elucidate the role of water in the dynamics of the solutes. Our results demonstrate that at low water concentrations (less than 5 wt. %), the plasticization phenomenon prevails for all the materials analyzed. However, at higher water concentrations, two different scenarios can be observed: the slaving phenomenon or plasticization, depending on the solute analyzed. These results generalize the slaving phenomenon to some, but not all, non-biological solutions and allow us to analyze the key factors for observing the slaving behavior in protein solutions as well as to reshaping the slaving concept.
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Affiliation(s)
- Izaskun Combarro Palacios
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
| | - Christoffer Olsson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | | | - Jan Swenson
- Department of Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Silvina Cerveny
- Centro de Física de Materiales (CSIC-UPV/EHU)-Material Physics Centre (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain
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Fan S, Ruggiero MT, Song Z, Qian Z, Wallace VP. Correlation between saturated fatty acid chain-length and intermolecular forces determined with terahertz spectroscopy. Chem Commun (Camb) 2019; 55:3670-3673. [PMID: 30855614 DOI: 10.1039/c9cc00141g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We measured crystalline (C-form) saturated fatty acids with even carbon numbers ranging from 12 to 20 using temperature dependent terahertz time-domain spectroscopy (THz-TDS). Absorption features between 0.5 and 3 THz were identified at temperatures from 96 K to 293 K, and a systematic red-shift was obvserved with the increasing carbon chain length. The origins of these absorption bands were uncovered using state-of-the-art ab initio density functional theory (DFT) calculations. Similar vibrational motions in the absorption bands of the different materials highlight the unique role that THz-TDS has for probing weak non-covalent interactions in these materials. Our results showcase the utility of the terahertz region, which is beyond the scope of related vibrational techniques, providing direct evidence of the effect of chain length on the intermolecular interactions of these molecules.
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Affiliation(s)
- Shuting Fan
- College of Electronic Science and Technology, Shenzhen University, 3688 Nanhai Rd, Shenzhen, Guangdong Province 518060, China.
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Functional Hydration Behavior: Interrelation between Hydration and Molecular Properties at Lipid Membrane Interfaces. J CHEM-NY 2019. [DOI: 10.1155/2019/4867327] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Water is an abundant commodity and has various important functions. It stabilizes the structure of biological macromolecules, controls biochemical activities, and regulates interfacial/intermolecular interactions. Common aspects of interfacial water can be obtained by overviewing fundamental functions and properties at different temporal and spatial scales. It is important to understand the hydrogen bonding and structural properties of water and to evaluate the individual molecular species having different hydration properties. Water molecules form hydrogen bonds with biomolecules and contribute to the adjustment of their properties, such as surface charge, hydrophilicity, and structural flexibility. In this review, the fundamental properties of water molecules and the methods used for the analyses of water dynamics are summarized. In particular, the interrelation between the hydration properties, determined by molecules, and the properties of molecules, determined by their hydration properties, are discussed using the lipid membrane as an example. Accordingly, interesting water functions are introduced that provide beneficial information in the fields of biochemistry, medicine, and food chemistry.
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Wei L, Yu L, Jiaoqi H, Guorong H, Yang Z, Weiling F. Application of terahertz spectroscopy in biomolecule detection. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.flm.2019.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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35
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Juste-Dolz A, do Nascimento NM, Monzó I, Grau-García E, Román-Ivorra JA, Lopez-Paz JL, Escorihuela J, Puchades R, Morais S, Gimenez-Romero D, Maquieira Á. New structural insights into the role of TROVE2 complexes in the on-set and pathogenesis of systemic lupus erythematosus determined by a combination of QCM-D and DPI. Anal Bioanal Chem 2018; 411:4709-4720. [PMID: 30317445 DOI: 10.1007/s00216-018-1407-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 12/13/2022]
Abstract
The mechanism of self-recognition of the autoantigen TROVE2, a common biomarker in autoimmune diseases, has been studied with a quartz crystal microbalance with dissipation monitoring (QCM-D) and dual polarization interferometry (DPI). The complementarity and remarkable analytical features of both techniques has allowed new insights into the onset of systemic lupus erythematosus (SLE) to be achieved at the molecular level. The in vitro study for SLE patients and healthy subjects suggests that anti-TROVE2 autoantibodies may undergo an antibody bipolar bridging. An epitope-paratope-specific binding initially occurs to activate a hidden Fc receptor in the TROVE2 tertiary structure. This bipolar mechanism may contribute to the pathogenic accumulation of anti-TROVE2 autoantibody immune complex in autoimmune disease. Furthermore, the specific calcium-dependent protein-protein bridges point out at how the TRIM21/TROVE2 association might occur, suggesting that the TROVE2 protein could stimulate the intracellular immune signaling via the TRIM21 PRY-SPRY domain. These findings may help to better understand the origins of the specificity and affinity of TROVE2 interactions, which might play a key role in the SLE pathogenesis. This manuscript gives one of the first practical applications of two novel functions (-df/dD and Δh/molec) for the analysis of the data provided by QCM-D and DPI. In addition, it is the first time that QCM-D has been used for mapping hidden Fc receptors as well as linear epitopes in a protein tertiary structure. Graphical abstract ᅟ.
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Affiliation(s)
- Augusto Juste-Dolz
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022, Valencia, Spain
| | - Noelle M do Nascimento
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022, Valencia, Spain
| | - Isidro Monzó
- Departamento de Química-Física, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain
| | - Elena Grau-García
- Departamento de Reumatología, Hospital Universitario y Politécnico La Fe, and Rheumatology Research Group, Instituto de Investigación Sanitaria La Fe, Avenida de Fernando Abril Martorell No 106, 46026, Valencia, Spain
| | - Jose A Román-Ivorra
- Departamento de Reumatología, Hospital Universitario y Politécnico La Fe, and Rheumatology Research Group, Instituto de Investigación Sanitaria La Fe, Avenida de Fernando Abril Martorell No 106, 46026, Valencia, Spain
| | - José Luis Lopez-Paz
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Jorge Escorihuela
- Departamento de Química Orgánica, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain
| | - Rosa Puchades
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Sergi Morais
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain
| | - David Gimenez-Romero
- Departamento de Química-Física, Universitat de València, C/ Dr. Moliner 50, 46100, Burjassot, Spain.
| | - Ángel Maquieira
- Departamento de Química, Universitat Politècnica de València, 46022, Valencia, Spain.
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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37
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Yang X, Shi J, Wang Y, Yang K, Zhao X, Wang G, Xu D, Wang Y, Yao J, Fu W. Label-free bacterial colony detection and viability assessment by continuous-wave terahertz transmission imaging. JOURNAL OF BIOPHOTONICS 2018; 11:e201700386. [PMID: 29633578 DOI: 10.1002/jbio.201700386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/03/2018] [Indexed: 05/16/2023]
Abstract
Timely and accurate bacterial detection is critical for various health and safety applications, which promotes the continuous development of versatile optical sensors for bacterial investigations. Here, we report a new strategy for bacterial colony sensing using terahertz (THz) imaging with minimal assay procedures. The proposed method utilizes the acute sensitivity of THz wave to the changes in the water content and cellular structures. Single bacterial colonies of 4 bacterial species were directly distinguished using THz imaging by utilizing their differences in THz absorption. In addition, the distribution of mixed bacterial samples has been demonstrated by THz imaging, which demonstrated that the target bacterium could be easily recognized. Furthermore, we investigated the differentiation of bacterial viability, which indicated that bacteria under different living states could be distinguished by THz imaging because of their different hydration levels and cellular structures. Our results suggest that THz imaging has the potential to be used for mixed bacterial sample detection and bacterial viability assessment in a label-free and nondestructive manner.
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Affiliation(s)
- Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jia Shi
- Institute of Laser and Optoelectronics, School of Precision Instrument and Optoelectronic Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Optoelectronic Information Science and Technology (Ministry of Education), Tianjin University, Tianjin, China
| | - Yuye Wang
- Institute of Laser and Optoelectronics, School of Precision Instrument and Optoelectronic Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Optoelectronic Information Science and Technology (Ministry of Education), Tianjin University, Tianjin, China
| | - Ke Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiang Zhao
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Guiyu Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Degang Xu
- Institute of Laser and Optoelectronics, School of Precision Instrument and Optoelectronic Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Optoelectronic Information Science and Technology (Ministry of Education), Tianjin University, Tianjin, China
| | - Yunxia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jianquan Yao
- Institute of Laser and Optoelectronics, School of Precision Instrument and Optoelectronic Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Optoelectronic Information Science and Technology (Ministry of Education), Tianjin University, Tianjin, China
| | - Weiling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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38
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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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Shadrack Jabes B, Klein R, Delle Site L. Structural Locality and Early Stage of Aggregation of Micelles in Water: An Adaptive Resolution Molecular Dynamics Study. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- B. Shadrack Jabes
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
| | - Rupert Klein
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
| | - Luigi Delle Site
- Institute for Mathematics Freie Universität Berlin D‐14195 Berlin Germany
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40
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Li Y, Lukács A, Bordács S, Móczár J, Nyitrai M, Hebling J. The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 191:8-15. [PMID: 28972911 DOI: 10.1016/j.saa.2017.09.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Low-frequency modes of L-Asp and L-Asn were studied in the range from 0.1 to 3.0THz using time-domain Terahertz spectroscopy and density functional theory calculation. The results show that PBE-D2 shows more success than BLYP-D2 in prediction of THz absorption spectra. To compare their low-frequency modes, we adopted "vibrational character ID strips" proposed by Schmuttenmaer and coworkers [Journal of Physical Chemistry B, 117, 10444(2013)]. We found that the most intense THz absorption peaks of two compounds both involve severe distortion of their hydrogen bonding networks. Due to less rigid hydrogen bonding network in L-Asp, the side chain (carboxyl group) of L-Asp exhibits larger motions than that (carboxamide group) of L-Asn in low-frequency modes.
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Affiliation(s)
- Yin Li
- MTA-PTE High-Field Terahertz Research Group, Ifjúság Street 6, Pécs H-7624, Hungary; Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - András Lukács
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - Sándor Bordács
- Department of Physics, Budapest University of Technology and Economics, Budafoki Street 8, Budapest H-1111, Hungary
| | - János Móczár
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - Miklós Nyitrai
- Department of Biophysics, University of Pécs, Szigeti Street 12, Pécs H-7624, Hungary
| | - János Hebling
- MTA-PTE High-Field Terahertz Research Group, Ifjúság Street 6, Pécs H-7624, Hungary; Department of Experimental Physics, University of Pécs, Ifjúság Street 6, H-7624 Pécs, Hungary.
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41
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Martin DR, Forsmo JE, Matyushov DV. Complex Dynamics of Water in Protein Confinement. J Phys Chem B 2017; 122:3418-3425. [PMID: 29206460 DOI: 10.1021/acs.jpcb.7b10448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper studies single-molecule and collective dynamics of water confined in protein powders by means of molecular dynamics simulations. The single-particle dynamics show a modest retardation compared to the bulk but become highly stretched in the powder, with the stretching exponent of ≃0.2. The collective dynamics of the total water dipole are affected by intermolecular correlations inside water and by cross-correlations between the water and the protein. The dielectric spectrum of water in the powder has two nearly equal-amplitude peaks: a Debye peak with ≃16 ps relaxation time and a highly stretched peak with the relaxation time of ≃13 ns and a stretching exponent of ≃0.12. The slower relaxation component is not seen in the single-molecule correlation functions and can be assigned to elastic protein motions displacing water in the powder. The loss spectrum of the intermediate scattering function reported by neutron-scattering experiments is also highly stretched, with the high-frequency wing scaling according to a power law. Translational dynamics can become much slower in the powder than in the bulk but are overshadowed by the rotational loss in the overall loss spectrum of neutron scattering.
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Affiliation(s)
| | - James E Forsmo
- College of Engineering , Georgia Institute of Technology , 225 North Avenue , Atlanta , Georgia 30332 , United States
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42
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Biomedical Applications of Terahertz Spectroscopy and Imaging. Trends Biotechnol 2017; 34:810-824. [PMID: 27207226 DOI: 10.1016/j.tibtech.2016.04.008] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/08/2016] [Accepted: 04/14/2016] [Indexed: 12/16/2022]
Abstract
Terahertz (THz=10(12)Hz) radiation has attracted wide attention for its unprecedented sensing ability and its noninvasive and nonionizing properties. Tremendous strides in THz instrumentation have prompted impressive breakthroughs in THz biomedical research. Here, we review the current state of THz spectroscopy and imaging in various biomedical applications ranging from biomolecules, including DNA/RNA, amino acids/peptides, proteins, and carbohydrates, to cells and tissues. We also address the potential biological effects of THz radiation during its biological applications and propose future prospects for this cutting-edge technology.
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Relative Contributions of Core Protein and Solvation Shell in the Terahertz Dielectric Properties of Protein Solutions. J Phys Chem B 2017; 121:9508-9512. [DOI: 10.1021/acs.jpcb.7b06442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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A label-free detector for liquid chromatography systems using mm-wave technology: First proof of concept. J Chromatogr A 2017; 1516:79-88. [DOI: 10.1016/j.chroma.2017.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/31/2017] [Accepted: 08/05/2017] [Indexed: 11/22/2022]
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45
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Martin DR, Matyushov DV. Terahertz absorption of lysozyme in solution. J Chem Phys 2017; 147:084502. [DOI: 10.1063/1.4989641] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel R. Martin
- Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287,
USA
| | - Dmitry V. Matyushov
- Department of Physics and School of Molecular Sciences, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287,
USA
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46
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Feng CJ, Tokmakoff A. The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study. J Chem Phys 2017; 147:085101. [PMID: 28863528 PMCID: PMC5593305 DOI: 10.1063/1.4991871] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/09/2017] [Indexed: 11/14/2022] Open
Abstract
We present a joint experimental and computational study of the dynamic interactions of dialanine (Ala-Ala) with water, comparing the results of ultrafast 2D IR and infrared transient absorption spectroscopy of its amide I vibration with spectra modeled from molecular dynamics (MD) simulations. The experimental data are analyzed to describe vibrational frequency fluctuations, vibrational energy relaxation, and chemical exchange processes. The origin of these processes in the same underlying fluctuating forces allows a common description in terms of the fluctuations and conformational dynamics of the peptide and associated solvent. By comparing computational spectroscopy from MD simulations with multiple force fields and water models, we describe how the dynamics of water hydrogen bond fluctuations and switching processes act as a source of friction that governs the dephasing and vibrational relaxation, and provide a description of coupled water and peptide motions that give rise to spectroscopic exchange processes.
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Affiliation(s)
- Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
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47
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Abstract
The structure and function of biomolecules are strongly influenced by their hydration shells. Structural fluctuations and molecular excitations of hydrating water molecules cover a broad range in space and time, from individual water molecules to larger pools and from femtosecond to microsecond time scales. Recent progress in theory and molecular dynamics simulations as well as in ultrafast vibrational spectroscopy has led to new and detailed insight into fluctuations of water structure, elementary water motions, electric fields at hydrated biointerfaces, and processes of vibrational relaxation and energy dissipation. Here, we review recent advances in both theory and experiment, focusing on hydrated DNA, proteins, and phospholipids, and compare dynamics in the hydration shells to bulk water.
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Affiliation(s)
- Damien Laage
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut
für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - James T. Hynes
- École
Normale Supérieure, PSL Research University, UPMC Univ Paris
06, CNRS, Département de Chimie,
PASTEUR, 24 rue Lhomond, 75005 Paris, France
- Sorbonne
Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France
- Department
of Chemistry and Biochemistry, University
of Colorado, Boulder, Colorado 80309, United
States
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Das Mahanta D, Samanta N, Mitra RK. Decisive Role of Hydrophobicity on the Effect of Alkylammonium Chlorides on Protein Stability: A Terahertz Spectroscopic Finding. J Phys Chem B 2017; 121:7777-7785. [DOI: 10.1021/acs.jpcb.7b04088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasish Das Mahanta
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
| | - Nirnay Samanta
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
| | - Rajib Kumar Mitra
- Chemical, Biological and
Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences Block-JD, Sector-III, Salt Lake, Kolkata, 700106, India
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Verma R, Mitchell-Koch K. In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function. Catalysts 2017; 7:212. [PMID: 30464857 PMCID: PMC6241538 DOI: 10.3390/catal7070212] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme-substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly.
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Affiliation(s)
- Rajni Verma
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
| | - Katie Mitchell-Koch
- Department of Chemistry, McKinley Hall, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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Laage D, Elsaesser T, Hynes JT. Perspective: Structure and ultrafast dynamics of biomolecular hydration shells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044018. [PMID: 28470026 PMCID: PMC5398927 DOI: 10.1063/1.4981019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 03/31/2017] [Indexed: 05/25/2023]
Abstract
The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.
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Affiliation(s)
- Damien Laage
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Départment de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
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