1
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Omwansu W, Musembi R, Derese S. Graph-based analysis of H-bond networks and unsupervised learning reveal conformational coupling in prion peptide segments. Phys Chem Chem Phys 2024. [PMID: 39291469 DOI: 10.1039/d4cp02123a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
In this study, we employed a comprehensive computational approach to investigate the physical chemistry of the water networks surrounding hydrated peptide segments, as derived from molecular dynamics simulations. Our analysis uncovers a complex interplay of direct and water-mediated hydrogen bonds that intricately weave through the peptides. We demonstrate that these hydrogen bond networks encode critical information about the peptides' conformational behavior, with the dimensionality of these networks showing sensitivity to the peptides' conformations. Additionally, we estimated the free-energy landscape of the peptides across various conformations, revealing that their structures are predominantly characterized by unfolded, partially folded, and folded configurations, resulting in broad and rugged free-energy surfaces due to the numerous degrees of freedom contributed by the surrounding solvent. Importantly, the structured nature of this free-energy landscape becomes obscured when conventional collective variables, such as the number of hydrogen bonds, are used. Our findings provide new insights into the molecular mechanisms that couple protein and solvent degrees of freedom, highlighting their significance in the functioning of biological systems.
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Affiliation(s)
- Wycliffe Omwansu
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Robinson Musembi
- Department of Physics, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya.
| | - Solomon Derese
- Department of Chemistry, University of Nairobi, P.O. Box 30197-00100, Nairobi, Kenya
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2
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Zehra, Hussain A, AlAjmi MF, Ishrat R, Hassan MI. Enriching Anticancer Drug Pipeline with Potential Inhibitors of Cyclin-Dependent Kinase-8 Identified from Natural Products. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:478-488. [PMID: 39149808 DOI: 10.1089/omi.2024.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Cyclin-dependent kinase 8 (CDK8) is highly expressed in various cancers and common complex human diseases, and an important therapeutic target for drug discovery and development. The CDK8 inhibitors are actively sought after, especially among natural products. We performed a virtual screening using the ZINC library comprising approximately 90,000 natural compounds. We applied Lipinski's rule of five, absorption, distribution, metabolism, excretion, and toxicity properties, and pan-assay interference compounds filter to eliminate promiscuous binders. Subsequently, the filtered compounds underwent molecular docking to predict their binding affinity and interactions with the CDK8 protein. Interaction analysis were carried out to elucidate the interaction mechanism of the screened hits with binding pockets of the CDK8. The ZINC02152165, ZINC04236005, and ZINC02134595 were selected with appreciable specificity and affinity with CDK8. An all-atom molecular dynamic (MD) simulation followed by essential dynamics was performed for 200 ns. Taken together, the results suggest that ZINC02152165, ZINC04236005, and ZINC02134595 can be harnessed as potential leads in therapeutic development. Moreover, the binding of the molecules brings change in protein conformation in a way that blocks the ATP-binding site of the protein, obstructing its kinase activity. These new findings from natural products offer insights into the molecular mechanisms underlying CDK8 inhibition. CDK8 was previously associated with behavioral and neurological diseases such as autism spectrum disorder, and cancers, for example, colorectal, prostate, breast, and acute myeloid leukemia. Hence, we call for further research and experimental validation, and with an eye to inform future clinical drug discovery and development in these therapeutic fields.
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Affiliation(s)
- Zehra
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Romana Ishrat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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3
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Tavagnacco L, Zanatta M, Buratti E, Bertoldo M, Chiessi E, Appel M, Natali F, Orecchini A, Zaccarelli E. Water slowing down drives the occurrence of the low temperature dynamical transition in microgels. Chem Sci 2024; 15:9249-9257. [PMID: 38903230 PMCID: PMC11186305 DOI: 10.1039/d4sc02650k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 06/22/2024] Open
Abstract
The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.
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Affiliation(s)
- Letizia Tavagnacco
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Marco Zanatta
- Department of Physics, University of Trento Via Sommarive 14 38123 Trento Italy
| | - Elena Buratti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata Via della Ricerca Scientifica I 00133 Rome Italy
| | - Markus Appel
- Institut Laue-Langevin 71 avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Francesca Natali
- CNR-IOM, Operative Group Grenoble (OGG), Institut Laue Langevin F-38042 Grenoble France
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
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4
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Bassotti E, Gabrielli S, Paradossi G, Chiessi E, Telling M. An experimentally representative in-silico protocol for dynamical studies of lyophilised and weakly hydrated amorphous proteins. Commun Chem 2024; 7:83. [PMID: 38609466 PMCID: PMC11014950 DOI: 10.1038/s42004-024-01167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Characterization of biopolymers in both dry and weakly hydrated amorphous states has implications for the pharmaceutical industry since it provides understanding of the effect of lyophilisation on stability and biological activity. Atomistic Molecular Dynamics (MD) simulations probe structural and dynamical features related to system functionality. However, while simulations in homogenous aqueous environments are routine, dehydrated model assemblies are a challenge with systems investigated in-silico needing careful consideration; simulated systems potentially differing markedly despite seemingly negligible changes in procedure. Here we propose an in-silico protocol to model proteins in lyophilised and weakly hydrated amorphous states that is both more experimentally representative and routinely applicable. Since the outputs from MD align directly with those accessed by neutron scattering, the efficacy of the simulation protocol proposed is shown by validating against experimental neutron data for apoferritin and insulin. This work also highlights that without cooperative experimental and simulative data, development of simulative procedures using MD alone would prove most challenging.
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Affiliation(s)
- Elisa Bassotti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Sara Gabrielli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Gaio Paradossi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133, Rome, Italy.
| | - Mark Telling
- STFC, ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, OX11OQX, UK.
- Department of Materials, University of Oxford, Parks Road, Oxford, UK.
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5
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Ghaedizadeh S, Zeinali M, Dabirmanesh B, Rasekh B, Khajeh K, Banaei-Moghaddam AM. Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140962. [PMID: 37716447 DOI: 10.1016/j.bbapap.2023.140962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies in order to increase the rate of CO2 absorption from the industrial flue gases is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from Sulfurihydrogenibium yellowstonense. Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.
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Affiliation(s)
- Shima Ghaedizadeh
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Majid Zeinali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Khosrow Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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6
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Sohmen B, Beck C, Frank V, Seydel T, Hoffmann I, Hermann B, Nüesch M, Grimaldo M, Schreiber F, Wolf S, Roosen‐Runge F, Hugel T. The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304262. [PMID: 37984887 PMCID: PMC10754087 DOI: 10.1002/advs.202304262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/06/2023] [Indexed: 11/22/2023]
Abstract
Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.
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Affiliation(s)
- Benedikt Sohmen
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Christian Beck
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Veronika Frank
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Tilo Seydel
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Ingo Hoffmann
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Bianca Hermann
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
| | - Mark Nüesch
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 190CH‐8057ZurichSwitzerland
| | - Marco Grimaldo
- Science DivisionInstitut Max von Laue ‐ Paul Langevin71 avenue des MartyrsGrenoble38042France
| | - Frank Schreiber
- Institute of Applied PhysicsUniversity of TübingenAuf der Morgenstelle 1072076TübingenGermany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of PhysicsUniversity of FreiburgHermann‐Herder‐Strasse 379104FreiburgGermany
| | - Felix Roosen‐Runge
- Department of Biomedical Sciences and Biofilms‐Research Center for Biointerfaces (BRCB)Malmö University20506MalmöSweden
- Division of Physical ChemistryLund UniversityNaturvetarvägen 1422100LundSweden
| | - Thorsten Hugel
- Institute of Physical ChemistryUniversity of FreiburgAlbertstrasse 2179104FreiburgGermany
- Signalling Research Centers BIOSS and CIBSSUniversity of FreiburgSchänzlestrasse 1879104FreiburgGermany
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7
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Chandra A, Kayal A, Das B, Chandra A. Dynamical Crossover of Interfacial Water upon Melting of a Lipid Bilayer: Influence of Different Parts of the Headgroups. J Phys Chem B 2023. [PMID: 38032152 DOI: 10.1021/acs.jpcb.3c04792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
All-atom molecular dynamics simulations of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine bilayer in contact with liquid water were performed at different temperatures ranging from 285 to 320 K. We have investigated the heterogeneity and dynamical transitions in interfacial water as the lipid bilayer undergoes a melting transition. Results are obtained for water at the outer surface of the bilayer and for those buried more deeply in the lipid chains of the bilayer. It is found that lipid bilayer melting influences both the structure and dynamics of interfacial water. The number of interfacial water molecules shows a jump in the melting of the bilayer. The temperature dependence of the diffusivity and orientational relaxation of interfacial water molecules exhibits a dynamical crossover upon melting of the bilayer. The extent of dynamical crossover is found to be rather strong with significant changes in activation barriers for interfacial water around the carbonyl groups, which are deeply buried toward the lipid chains of the bilayer. The dynamical crossover gradually decreases as one moves further away from the outer surface, and it essentially vanishes for water in the region of 5-10 Å from the outer surface. It is found that the lipid melting-induced dynamical crossover of interfacial water is significant only for water that is in close proximity to the bilayer surface or deeply buried into it. The current results reveal that water molecules in different parts of the interface respond differently on melting of the bilayer. The current study also shows that the carbonyl-bound water molecules can play an important role in the phase transition of the bilayer as the temperature is raised through its melting point.
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Affiliation(s)
- Abhilash Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Abhijit Kayal
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Banshi Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Uttar Pradesh 208016, India
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8
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Sauer MA, Heyden M. Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins. J Chem Theory Comput 2023; 19:5481-5490. [PMID: 37515568 PMCID: PMC10624555 DOI: 10.1021/acs.jctc.2c01309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2023]
Abstract
Low-frequency molecular vibrations at far-infrared frequencies are thermally excited at room temperature. As a consequence, thermal fluctuations are not limited to the immediate vicinity of local minima on the potential energy surface, and anharmonic properties cannot be ignored. The latter is particularly relevant in molecules with multiple conformations, such as proteins and other biomolecules. However, existing theoretical and computational frameworks for the analysis of molecular vibrations have so far been limited by harmonic or quasi-harmonic approximations, which are ill-suited to describe anharmonic low-frequency vibrations. Here, we introduce a fully anharmonic analysis of molecular vibrations based on a time correlation formalism that eliminates the need for harmonic or quasi-harmonic approximations. We use molecular dynamics simulations of a small protein to demonstrate that this new approach, in contrast to harmonic and quasi-harmonic normal modes, correctly identifies the collective degrees of freedom associated with molecular vibrations at any given frequency. This allows us to unambiguously characterize the anharmonic character of low-frequency vibrations in the far-infrared spectrum.
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Affiliation(s)
- Michael A Sauer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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9
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Ohkubo T, Komiyama N, Masu H, Kishikawa K, Kohri M. Molecular Dynamics Studies of the Ho(III) Aqua-tris(dibenzoylmethane) Complex: Role of Water Dynamics. Inorg Chem 2023. [PMID: 37470095 DOI: 10.1021/acs.inorgchem.3c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
The seven-coordinate Ho(III) aqua-tris(dibenzoylmethane)(DBM) complex, referred to as Ho-(DBM)3·H2O, was first reported in the late 1960s. It has a threefold symmetric structure, with Ho at the center of three dibenzoylmethane ligands and hydrogen-bonded water to ligands. It is considered that the hydrogen bonds between the water molecule and the ligands surrounding Ho play an important role in the formation of its symmetrical structure. In this work, we developed new force-field parameters for classical molecular dynamics (CMD) simulations to theoretically elucidate the structure and dynamics of Ho-(DBM)3·H2O. To develop the force field, structural optimization and molecular dynamics were performed on the basis of ab initio calculations using the plane-wave pseudopotential method. The force-field parameters for CMD were then optimized to reproduce the data obtained from ab initio calculations. Validation of the developed force field showed good agreement with the experimental crystalline structure and ab initio data. The vibrational properties of water in Ho-(DBM)3·H2O were investigated by comparison with bulk liquid water. The vibrational motion of water was found to have a characteristic mode originating from stationary rotational motion along the c-axis of Ho(III) aqua-tris(dibenzoylmethane). Contrary to expectations, the hydrogen-bond dynamics of water in Ho-(DBM)3·H2O were found to be almost equivalent to those of bulk liquid water except for librational motion. This development route for force-field parameters for CMD and the establishment of water dynamics can advance the understanding of water-coordinated metal complexes with high coordination numbers such as Ho-(DBM)3·H2O.
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Affiliation(s)
- Takahiro Ohkubo
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho Inage-ku, Chiba 263-8522, Japan
| | - Nao Komiyama
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho Inage-ku, Chiba 263-8522, Japan
| | - Hyuma Masu
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho Inage-ku, Chiba 263-8522, Japan
| | - Keiki Kishikawa
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho Inage-ku, Chiba 263-8522, Japan
| | - Michinari Kohri
- Graduate School of Engineering, Chiba University, 1-33 Yayoi-cho Inage-ku, Chiba 263-8522, Japan
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10
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Ganesan V, Priya MH. Probing the Conformational Preference to β-Strand during Peptide Self-Assembly. J Phys Chem B 2023. [PMID: 37364023 DOI: 10.1021/acs.jpcb.3c02327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Alanine-rich tetrapeptides like A3K dominantly exist as polyproline II helices in dilute aqueous solutions. However, during self-assembly, based on the free energy calculation in implicit solvent for various peptide conformations, only the peptides in the β-strand conformation can be packed closely. This necessitates the conformational transition to the β-strand commonly observed during peptide self-assembly such as in amyloid fibril formation. In fact, the closest interpeptide distance of 4.8 Å is consistent with the interstrand distance determined from the X-ray diffraction pattern of many amyloid fibrils. The position of free energy minimum obtained from implicit solvent calculation matches exactly with the explicit solvent simulation through umbrella sampling when the peptide conformations are restrained, demonstrating the applicability of the former for rapid screening of peptide configurations favorable for self-assembly. The barrier in the free energy profile in the presence of water arises out of the entropic restriction on the interstitial water molecules while satisfying the hydrogen bonding of both the peptides by forming water mediated hydrogen bond bridge. Further, the high energy barrier observed for the β-strand suggests that peptides initially tend to self-assemble in the polyproline II structure to mitigate the desolvation energy cost; the transition to the β-strand would happen only in the later stage after crossing the barrier. The umbrella sampling simulations with peptides allowed to change conformations, relative to each other, confirm the dynamic conformational transition during the course of the self-assembly supporting the "dock and lock" mechanism suggested for amyloid fibrillar growth.
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Affiliation(s)
- Vidhya Ganesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - M Hamsa Priya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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11
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Diaz A, Ramakrishnan V. Effect of osmolytes on the EcoRI endonuclease: Insights into hydration and protein dynamics from molecular dynamics simulations. Comput Biol Chem 2023; 105:107883. [PMID: 37210944 DOI: 10.1016/j.compbiolchem.2023.107883] [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: 01/13/2023] [Revised: 05/16/2023] [Accepted: 05/16/2023] [Indexed: 05/23/2023]
Abstract
Osmolytes play an important role in cellular physiology by modulating the properties of proteins, including their molecular specificity. EcoRI is a model restriction enzyme whose specificity to DNA is altered in the presence of osmolytes. Here, we investigate the effect of two different osmolytes, glycerol and DMSO, on the dynamics and hydration of the EcoRI enzyme using molecular dynamics simulations. Our results show that the osmolytes, alter the essential dynamics of EcoRI. Particularly, we observe that the dynamics of the arm region of EcoRI which is involved in DNA binding is significantly altered. In addition, conformational free energy analyses reveals that the osmolytes bring about a change in the landscape similar to that of EcoRI bound to cognate DNA. We further observe that the hydration of the enzyme for each of the osmolyte is different, indicating that the mechanism of action of each of these osmolytes could be different. Further analyses of interfacial water dynamics using rotational autocorrelation function reveals that while the protein surface contributes to a slower tumbling motion of water, osmolytes, additionally contribute to the slowing of the angular motion of the water molecules. Entropy analysis also corroborates with this finding. We also find that the slowed rotational motion of interfacial waters in the presence of osmolytes contributes to a slowed relaxation of the hydrogen bonds between the interfacial waters and the functionally important residues in the protein. Taken together, our results show that osmolytes alter the dynamics of the protein by altering the dynamics of water. This altered dynamics, mediated by the changes in the water dynamics and hydrogen bonds with functionally important residues, may contribute to the altered specificity of EcoRI in the presence of osmolytes.
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Affiliation(s)
- Aathithya Diaz
- Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India
| | - Vigneshwar Ramakrishnan
- Computational Molecular Biophysics Laboratory, Bioinformatics Center, School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur 613401, Tamil Nadu, India.
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12
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Onvlee J, Trippel S, Küpper J. Ultrafast light-induced dynamics in the microsolvated biomolecular indole chromophore with water. Nat Commun 2022; 13:7462. [PMID: 36460654 PMCID: PMC9718776 DOI: 10.1038/s41467-022-33901-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/04/2022] [Indexed: 12/05/2022] Open
Abstract
Interactions between proteins and their solvent environment can be studied in a bottom-up approach using hydrogen-bonded chromophore-solvent clusters. The ultrafast dynamics following UV-light-induced electronic excitation of the chromophores, potential radiation damage, and their dependence on solvation are important open questions. The microsolvation effect is challenging to study due to the inherent mix of the produced gas-phase aggregates. We use the electrostatic deflector to spatially separate different molecular species in combination with pump-probe velocity-map-imaging experiments. We demonstrate that this powerful experimental approach reveals intimate details of the UV-induced dynamics in the near-UV-absorbing prototypical biomolecular indole-water system. We determine the time-dependent appearance of the different reaction products and disentangle the occurring ultrafast processes. This approach ensures that the reactants are well-known and that detailed characteristics of the specific reaction products are accessible - paving the way for the complete chemical-reactivity experiment.
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Affiliation(s)
- Jolijn Onvlee
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Sebastian Trippel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
- Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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13
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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14
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Konstantinovsky D, Perets EA, Santiago T, Velarde L, Hammes-Schiffer S, Yan ECY. Detecting the First Hydration Shell Structure around Biomolecules at Interfaces. ACS CENTRAL SCIENCE 2022; 8:1404-1414. [PMID: 36313165 PMCID: PMC9615115 DOI: 10.1021/acscentsci.2c00702] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 05/15/2023]
Abstract
Understanding the role of water in biological processes remains a central challenge in the life sciences. Water structures in hydration shells of biomolecules are difficult to study in situ due to overwhelming background from aqueous environments. Biological interfaces introduce additional complexity because biomolecular hydration differs at interfaces compared to bulk solution. Here, we perform experimental and computational studies of chiral sum frequency generation (chiral SFG) spectroscopy to probe chirality transfer from a protein to the surrounding water molecules. This work reveals that chiral SFG probes the first hydration shell around the protein almost exclusively. We explain the selectivity to the first hydration shell in terms of the asymmetry induced by the protein structure and specific protein-water hydrogen-bonding interactions. This work establishes chiral SFG as a powerful technique for studying hydration shell structures around biomolecules at interfaces, presenting new possibilities to address grand research challenges in biology, including the molecular origins of life.
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Affiliation(s)
- Daniel Konstantinovsky
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ethan A. Perets
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ty Santiago
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Luis Velarde
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | | | - Elsa C. Y. Yan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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15
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Lyu T, Sohn SH, Jimenez R, Joo T. Temperature-Dependent Fluorescence of mPlum Fluorescent Protein from 295 to 20 K. J Phys Chem B 2022; 126:2337-2344. [PMID: 35296137 DOI: 10.1021/acs.jpcb.1c10516] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of bright fluorescent proteins (FPs) emitting beyond 600 nm continues to be of interest both from a fundamental perspective in understanding protein-chromophore interactions and from a practical perspective as these FPs would be valuable for cellular imaging. We previously reported ultrafast spectral observations of the excited-state dynamics in mPlum resulting from interconversion between direct hydrogen bonding and water-mediated hydrogen bonding between the chromophore acylimine carbonyl and the Glu16 side chain. Here, we report temperature-dependent steady-state and time-resolved fluorescence measurements of mPlum and its E16H variant, which does not contain a side-chain permitting hydrogen bonding with the acylimine carbonyl. Lowering the temperature of the system freezes interconversion between the hydrogen-bonding states, thus revealing the spectral signatures of the two states. Analysis of the temperature-dependent spectra assuming Boltzmann populations of the two states yields a 205 cm-1 energy difference. This value agrees with the predictions from a quantum mechanics/molecular mechanics study of mPlum (198 cm-1). This study demonstrates the first use of cryogenic spectroscopy to quantify the energetics and timescales of FP chromophore structural states that were only previously obtained from computational methods and further confirms the importance of acylimine hydrogen-bonding dynamics to the fluorescence spectral shifts of red FPs.
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Affiliation(s)
- Taecheon Lyu
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - So Hyeong Sohn
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Ralph Jimenez
- JILA, University of Colorado, and NIST, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Taiha Joo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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16
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Steinert RM, Kasireddy C, Heikes ME, Mitchell-Koch KR. Newly identified C–H⋯O hydrogen bond in histidine. Phys Chem Chem Phys 2022; 24:19233-19251. [DOI: 10.1039/d2cp02048c] [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
Histidine C–H bonds observed in protein structures include (clockwise from top left): myoglobin, β-lactamase, and photoactive yellow protein; calculations indicate that tautomeric/protonation state influences H-bonding ability (bottom left).
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Affiliation(s)
- Ryan M. Steinert
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Chandana Kasireddy
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Micah E. Heikes
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
| | - Katie R. Mitchell-Koch
- Department of Chemistry and Biochemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, USA
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17
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Shrestha UR, Mamontov E, O'Neill HM, Zhang Q, Kolesnikov AI, Chu X. Experimental mapping of short-wavelength phonons in proteins. Innovation (N Y) 2022; 3:100199. [PMID: 35059681 PMCID: PMC8760453 DOI: 10.1016/j.xinn.2021.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Phonons are quasi-particles, observed as lattice vibrations in periodic materials, that often dampen in the presence of structural perturbations. Nevertheless, phonon-like collective excitations exist in highly complex systems, such as proteins, although the origin of such collective motions has remained elusive. Here we present a picture of temperature and hydration dependence of collective excitations in green fluorescent protein (GFP) obtained by inelastic neutron scattering. Our results provide evidence that such excitations can be used as a measure of flexibility/softness and are possibly associated with the protein’s activity. Moreover, we show that the hydration water in GFP interferes with the phonon propagation pathway, enhancing the structural rigidity and stability of GFP. Quantum phenomena in biology have long fascinated people around the world This work presents a direct experimental observation of phonons, the quantum vibrations in a protein The collective excitations or phonons in proteins were detected by utilizing inelastic neutron scattering technique at Oak Ridge National Laboratory Our results illustrate the flexibility-activity relationship in proteins by mapping the temperature and hydration dependence of these collective excitations
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Affiliation(s)
- Utsab R. Shrestha
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eugene Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hugh M. O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Xiangqiang Chu
- Department of Nuclear Science and Technology, Graduate School of China Academy of Engineering Physics, Beijing 100193, China
- Corresponding author
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18
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Bin M, Yousif R, Berkowicz S, Das S, Schlesinger D, Perakis F. Wide-angle X-ray scattering and molecular dynamics simulations of supercooled protein hydration water. Phys Chem Chem Phys 2021; 23:18308-18313. [PMID: 34269785 DOI: 10.1039/d1cp02126e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the mechanism responsible for the protein low-temperature crossover observed at T≈ 220 K can help us improve current cryopreservation technologies. This crossover is associated with changes in the dynamics of the system, such as in the mean-squared displacement, whereas experimental evidence of structural changes is sparse. Here we investigate hydrated lysozyme proteins by using a combination of wide-angle X-ray scattering and molecular dynamics (MD) simulations. Experimentally we suppress crystallization by accurate control of the protein hydration level, which allows access to temperatures down to T = 175 K. The experimental data indicate that the scattering intensity peak at Q = 1.54 Å-1, attributed to interatomic distances, exhibits temperature-dependent changes upon cooling. In the MD simulations it is possible to decompose the water and protein contributions and we observe that, while the protein component is nearly temperature independent, the hydration water peak shifts in a fashion similar to that of bulk water. The observed trends are analysed by using the water-water and water-protein radial distribution functions, which indicate changes in the local probability density of hydration water.
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Affiliation(s)
- Maddalena Bin
- Department of Physics, AlbaNova University Center, Stockholm University, 106 91 Stockholm, Sweden.
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19
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Chan JC, Zhang B, Martinez M, Kuruba B, Brozik J, Kang C, Zhang X. Structural studies of Myceliophthora Thermophila Laccase in the presence of deep eutectic solvents. Enzyme Microb Technol 2021; 150:109890. [PMID: 34489043 DOI: 10.1016/j.enzmictec.2021.109890] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022]
Abstract
In this work, we elucidated the interactions between Myceliophthora thermophila laccase and deep eutectic solvent (DES) by crystallographic and kinetics analyses. Four types of DESs with different hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD), including lactic acid: betaine, glycerol: choline chloride, lactic acid: choline chloride and glycerol: betaine was used. The results revealed that different DES have different effects on laccase activity. Lactic acid-betaine (2:1) DES has shown to enhance laccase activity up to 300 % at a concentration ranged from 2% to 8% v/v, while glycerol: choline chloride and lactic acid: choline chloride DES choline chloride-based DES have found to possess inhibitory effects on laccase under the same concentration range. Detailed kinetic study showed that glycerol: choline chloride DES is a S-parabolic-I-parabolic mixed non-competitive inhibitor, where conformational changes can occur. The crystal structures of laccase with lactic acid: choline chloride DES (LCDES) were obtained at 1.6 Å. Crystallographic analysis suggested that the addition of LCDES causes changes in the laccase active site, but the increase in water molecules observed in the resulting crystal prevented laccase from experiencing drastic structural change. Fluorescence and circular dichroism spectroscopies were also applied to determine the effects of DES on the structural conformation of laccase. The results have confirmed that the presence of DES can trigger changes in the local environments of the amino acids in the active site of laccase which contributes to the changes in its activity and stability.
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Affiliation(s)
- Jou Chin Chan
- Voiland School of Chemical Engineering and Bioengineering - Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA
| | - Bixia Zhang
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Michael Martinez
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Balaganesh Kuruba
- Voiland School of Chemical Engineering and Bioengineering - Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA
| | - James Brozik
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA, 99164, USA.
| | - Xiao Zhang
- Voiland School of Chemical Engineering and Bioengineering - Washington State University, 2710 Crimson Way, Richland, WA, 99354, USA; Pacific Northwest National Laboratory - 902 Battelle Boulevard, P.O. Box 999, MSIN P8-60, Richland, WA, 99352, USA.
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20
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Liu H, Xiang S, Zhu H, Li L. The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation. Molecules 2021; 26:molecules26175403. [PMID: 34500836 PMCID: PMC8434405 DOI: 10.3390/molecules26175403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/01/2022] Open
Abstract
The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.
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Affiliation(s)
- Hangxin Liu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Shuqing Xiang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
| | - Haomiao Zhu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
| | - Li Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Nanjing 210023, China; (H.L.); (S.X.)
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Nanjing 210023, China
- Jiangsu Engineering Research Center for Biomedical Function Materials, Nanjing 210023, China
- Jiangsu Key Laboratory of Biofunctional Materials, Nanjing 210023, China
- School of Chemistry and Materials Science, Nanjing Normal University, No. 1 Wenyuan Road, Nanjing 210023, China
- Correspondence: (H.Z.); (L.L.)
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21
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Morón M. Protein hydration shell formation: Dynamics of water in biological systems exhibiting nanoscopic cavities. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Quan K, Hou J, Zhang Z, Ren Y, Peterson BW, Flemming HC, Mayer C, Busscher HJ, van der Mei HC. Water in bacterial biofilms: pores and channels, storage and transport functions. Crit Rev Microbiol 2021; 48:283-302. [PMID: 34411498 DOI: 10.1080/1040841x.2021.1962802] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Bacterial biofilms occur in many natural and industrial environments. Besides bacteria, biofilms comprise over 70 wt% water. Water in biofilms occurs as bound- or free-water. Bound-water is adsorbed to bacterial surfaces or biofilm (matrix) structures and possesses different Infra-red and Nuclear-Magnetic-Resonance signatures than free-water. Bound-water is different from intra-cellularly confined-water or water confined within biofilm structures and bacteria are actively involved in building water-filled structures by bacterial swimmers, dispersion or lytic self-sacrifice. Water-filled structures can be transient due to blocking, resulting from bacterial growth, compression or additional matrix formation and are generally referred to as "channels and pores." Channels and pores can be distinguished based on mechanism of formation, function and dimension. Channels allow transport of nutrients, waste-products, signalling molecules and antibiotics through a biofilm provided the cargo does not adsorb to channel walls and channels have a large length/width ratio. Pores serve a storage function for nutrients and dilute waste-products or antimicrobials and thus should have a length/width ratio close to unity. The understanding provided here on the role of water in biofilms, can be employed to artificially engineer by-pass channels or additional pores in industrial and environmental biofilms to increase production yields or enhance antimicrobial penetration in infectious biofilms.
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Affiliation(s)
- Kecheng Quan
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, P.R. China
| | - Jiapeng Hou
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Zexin Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, P.R. China
| | - Yijin Ren
- Department of Orthodontics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Brandon W Peterson
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences/Engineering and the School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Faculty of Chemistry, Biofilm Centre, University of Duisburg-Essen, Essen, Germany
| | - Christian Mayer
- Faculty of Chemistry, Physical Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Henk J Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Henny C van der Mei
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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23
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Community evolution and frequent subgraph patterns affect the thermostability of B. subtilis lipase A. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.100984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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24
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Hassan I, Ferraro F, Imhof P. Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021; 26:2148. [PMID: 33917998 PMCID: PMC8068333 DOI: 10.3390/molecules26082148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
The vibrational spectrum of the Ala-Leu-Ala-Leu peptide in solution, computed from first-principles simulations, shows a prominent band in the amide I region that is assigned to stretching of carbonyl groups. Close inspection reveals combined but slightly different contributions by the three carbonyl groups of the peptide. The shift in their exact vibrational signature is in agreement with the different probabilities of these groups to form hydrogen bonds with the solvent. The central carbonyl group has a hydrogen bond probability intermediate to the other two groups due to interchanges between different hydrogen-bonded states. Analysis of the interaction energies of individual water molecules with that group shows that shifts in its frequency are directly related to the interactions with the water molecules in the first hydration shell. The interaction strength is well correlated with the hydrogen bond distance and hydrogen bond angle, though there is no perfect match, allowing geometrical criteria for hydrogen bonds to be used as long as the sampling is sufficient to consider averages. The hydrogen bond state of a carbonyl group can therefore serve as an indicator of the solvent's effect on the vibrational frequency.
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Affiliation(s)
- Irtaza Hassan
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
| | - Federica Ferraro
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
| | - Petra Imhof
- Institute for Theoretical Physics, Freie Universtiät Berlin, Arnimallee 14, 14195 Berlin, Germany;
- Computer Chemistry Center, Friedrich-Alexander University (FAU) Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052 Erlangen, Germany;
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25
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Zhai Y, Luo P, Nagao M, Nakajima K, Kikuchi T, Kawakita Y, Kienzle PA, Z Y, Faraone A. Relevance of hydrogen bonded associates to the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol. Phys Chem Chem Phys 2021; 23:7220-7232. [PMID: 33876082 DOI: 10.1039/d0cp05481j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of approximately several Ångstroms, employing static and quasi-elastic neutron scattering and molecular dynamics simulation. Dynamic neutron scattering measurements were performed over an exchanged wave-vector range encompassing the pre-peak, indicative of the presence of H-bonding associates, and the main peak. The dynamics observed at the pre-peak is associated with the formation and disaggregation of the H-bonded associates and is measured to be at least one order of magnitude slower than the dynamics at the main peak, which is identified as the structural relaxation. The measurements indicate that the macroscopic shear viscosity has a similar temperature dependence as the dynamics of the H-bonded associates, which highlights the important role played by these structures, together with the structural relaxation, in defining the macroscopic rheological properties of the system. Importantly, the characteristic relaxation time at the pre-peak follows an Arrhenius temperature dependence whereas at the main peak it exhibits a non-Arrhenius behavior on approaching the supercooled state. The origin of this differing behavior is attributed to an increased structuring of the hydrophobic domains of 2-propanol accommodating a more and more encompassing H-bond network, and a consequent set in of dynamic cooperativity.
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Affiliation(s)
- Yanqin Zhai
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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26
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Steinrücken E, Wissel T, Brodrecht M, Breitzke H, Regentin J, Buntkowsky G, Vogel M. 2H NMR study on temperature-dependent water dynamics in amino-acid functionalized silica nanopores. J Chem Phys 2021; 154:114702. [PMID: 33752372 DOI: 10.1063/5.0044141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We prepare various amino-acid functionalized silica pores with diameters of ∼6 nm and study the temperature-dependent reorientation dynamics of water in these confinements. Specifically, we link basic Lys, neutral Ala, and acidic Glu to the inner surfaces and combine 2H nuclear magnetic resonance spin-lattice relaxation and line shape analyses to disentangle the rotational motions of the surfaces groups and the crystalline and liquid water fractions coexisting below partial freezing. Unlike the crystalline phase, the liquid phase shows reorientation dynamics, which strongly depends on the chemistry of the inner surfaces. The water reorientation is slowest for the Lys functionalization, followed by Ala and Glu and, finally, the native silica pores. In total, the rotational correlation times of water at the different surfaces vary by about two orders of magnitude, where this span is largely independent of the temperature in the range ∼200-250 K.
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Affiliation(s)
- Elisa Steinrücken
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Till Wissel
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Martin Brodrecht
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Hergen Breitzke
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Julia Regentin
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Gerd Buntkowsky
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, 64287 Darmstadt, Germany
| | - Michael Vogel
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
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27
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Schirò G, Fichou Y, Brogan APS, Sessions R, Lohstroh W, Zamponi M, Schneider GJ, Gallat FX, Paciaroni A, Tobias DJ, Perriman A, Weik M. Diffusivelike Motions in a Solvent-Free Protein-Polymer Hybrid. PHYSICAL REVIEW LETTERS 2021; 126:088102. [PMID: 33709739 DOI: 10.1103/physrevlett.126.088102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 01/11/2021] [Indexed: 05/16/2023]
Abstract
The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with water translational motions enabling protein flexibility. Engineered solvent-free protein-polymer hybrids have been shown to preserve protein structure, function, and dynamics. Here, we used neutron scattering, protein and polymer perdeuteration, and molecular dynamics simulations to explore how a polymer dynamically replaces water. Even though relaxation rates and vibrational properties are strongly modified in polymer coated compared to hydrated proteins, liquidlike polymer dynamics appear to plasticize the conjugated protein in a qualitatively similar way as do hydration-water translational motions.
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Affiliation(s)
- Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Yann Fichou
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN) UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600 Pessac, France
| | - Alex P S Brogan
- School of Biochemistry, Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Richard Sessions
- Department of Chemistry, King's College London, Britannia House, London SE1 1DB, United Kingdom
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Garching, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Gerald J Schneider
- Department of Chemistry and Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - François-Xavier Gallat
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, California, CA 92697, USA
| | - Adam Perriman
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
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28
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Perakis F, Gutt C. Towards molecular movies with X-ray photon correlation spectroscopy. Phys Chem Chem Phys 2021; 22:19443-19453. [PMID: 32870200 DOI: 10.1039/d0cp03551c] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective article we highlight research opportunities and challenges in probing structural dynamics of molecular systems using X-ray Photon Correlation Spectroscopy (XPCS). The development of new X-ray sources, such as 4th generation storage rings and X-ray free-electron lasers (XFELs), provides promising new insights into molecular motion. Employing XPCS at these sources allows to capture a very broad range of timescales and lengthscales, spanning from femtoseconds to minutes and atomic scales to the mesoscale. Here, we discuss the scientific questions that can be addressed with these novel tools for two prominent examples: the dynamics of proteins in biomolecular condensates and the dynamics of supercooled water. Finally, we provide practical tips for designing and estimating feasibility of XPCS experiments as well as on detecting and mitigating radiation damage.
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Affiliation(s)
- Fivos Perakis
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Christian Gutt
- Department Physik, Universität Siegen, D-57072 Siegen, Germany.
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29
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Giubertoni G, Burla F, Bakker HJ, Koenderink GH. Connecting the Stimuli-Responsive Rheology of Biopolymer Hydrogels to Underlying Hydrogen-Bonding Interactions. Macromolecules 2020; 53:10503-10513. [PMID: 33335340 PMCID: PMC7735748 DOI: 10.1021/acs.macromol.0c01742] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/04/2020] [Indexed: 11/29/2022]
Abstract
Many biopolymer hydrogels are environmentally responsive because they are held together by physical associations that depend on pH and temperature. Here, we investigate how the pH and temperature responses of the rheology of hyaluronan hydrogels are connected to the underlying molecular interactions. Hyaluronan is an essential structural biopolymer in the human body with many applications in biomedicine. Using two-dimensional infrared spectroscopy, we show that hyaluronan chains become connected by hydrogen bonds when the pH is changed from 7.0 to 2.5 and that the bond density at pH 2.5 is independent of temperature. Temperature-dependent rheology measurements show that because of this hydrogen bonding the stress relaxation at pH 2.5 is strongly slowed down in comparison to pH 7.0, consistent with the sticky reptation model of associative polymers. From the flow activation energy, we conclude that each polymer is cross-linked by multiple (5-15) hydrogen bonds to others, causing slow macroscopic stress relaxation, despite the short time scale of breaking and reformation of each individual hydrogen bond. Our findings can aid the design of stimuli-responsive hydrogels with tailored viscoelastic properties for biomedical applications.
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Affiliation(s)
| | - Federica Burla
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Huib J. Bakker
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Gijsje H. Koenderink
- AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
- Department of Bionanoscience, Kavli Institute
of Nanoscience Delft, Delft University of
Technology, Van der Maasweg 9, Delft 2629 HZ, The Netherlands
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30
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Shen D, Duley WW, Peng P, Xiao M, Feng J, Liu L, Zou G, Zhou YN. Moisture-Enabled Electricity Generation: From Physics and Materials to Self-Powered Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2003722. [PMID: 33185944 DOI: 10.1002/adma.202003722] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/11/2020] [Indexed: 05/24/2023]
Abstract
The exploration of the utilization of sustainable, green energy represents one way in which it is possible to ameliorate the growing threat of the global environmental issues and the crisis in energy. Moisture, which is ubiquitous on Earth, contains a vast reservoir of low-grade energy in the form of gaseous water molecules and water droplets. It has now been found that a number of functionalized materials can generate electricity directly from their interaction with moisture. This suggests that electrical energy can be harvested from atmospheric moisture and enables the creation of a new range of self-powered devices. Herein, the basic mechanisms of moisture-induced electricity generation are discussed, the recent advances in materials (including carbon nanoparticles, graphene materials, metal oxide nanomaterials, biofibers, and polymers) for harvesting electrical energy from moisture are summarized, and some strategies for improving energy conversion efficiency and output power in these devices are provided. The potential applications of moisture electrical generators in self-powered electronics, healthcare, security, information storage, artificial intelligence, and Internet-of-things are also discussed. Some remaining challenges are also considered, together with a number of suggestions for potential new developments of this emerging technology.
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Affiliation(s)
- Daozhi Shen
- Institute for Quantum Computing, Department of Chemistry, Centre for Advanced Materials Joining, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Walter W Duley
- Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Peng Peng
- School of Mechanical Engineering and Automation, Beihang University, Beijing, 100191, P. R. China
| | - Ming Xiao
- Centre for Advanced Materials Joining, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Jiayun Feng
- Centre for Advanced Materials Joining, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Lei Liu
- State Key Laboratory of Tribology, Tsinghua University, Beijing, 100084, P. R. China
| | - Guisheng Zou
- State Key Laboratory of Tribology, Tsinghua University, Beijing, 100084, P. R. China
| | - Y Norman Zhou
- Centre for Advanced Materials Joining, Waterloo Institute for Nanotechnology, Department of Mechanical and Mechatronics Engineering, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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Samantray S, Yin F, Kav B, Strodel B. Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:6462-6475. [DOI: 10.1021/acs.jcim.0c01063] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suman Samantray
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
- AICES Graduate School, RWTH Aachen University, Schinkelstraße 2, 52062 Aachen, Germany
| | - Feng Yin
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
| | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
| | - Birgit Strodel
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülch, 52428 Jülich, Germany
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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32
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Zhang Y, Hu W, Sun J, Li Y, Chen C. Hydrogen bonds and hydrate interaction between RiAFP and water revealed by molecular dynamics simulations. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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33
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Tian R, Hu G, Ou X, Luo M, Li J. Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface. J Chem Phys 2020; 153:124705. [PMID: 33003729 DOI: 10.1063/5.0019135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.
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Affiliation(s)
- Ranran Tian
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Guorong Hu
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Mengbo Luo
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Institute of Quantitative Biology, Department of Physics, Zhejiang University, Hangzhou 310027, China
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34
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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35
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Kämpf K, Demuth D, Zamponi M, Wuttke J, Vogel M. Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin. J Chem Phys 2020; 152:245101. [PMID: 32610976 DOI: 10.1063/5.0011107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about Em = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with Em = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τβ ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition Tg = 320 K of hydrated elastin, where the α relaxation of the protein obeys τα ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.
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Affiliation(s)
- Kerstin Kämpf
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Dominik Demuth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Joachim Wuttke
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
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36
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Influence of crowding agents on the dynamics of a multidomain protein in its denatured state: a solvation approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 49:289-305. [PMID: 32399581 DOI: 10.1007/s00249-020-01435-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/26/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023]
Abstract
It is now well appreciated that the crowded intracellular environment significantly modulates an array of physiological processes including protein folding-unfolding, aggregation, and dynamics to name a few. In this work we have studied the dynamics of domain I of the protein human serum albumin (HSA) in its urea-induced denatured states, in the presence of a series of commonly used macromolecular crowding agents. HSA was labeled at Cys-34 (a free cysteine) in domain I with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (BADAN) to act as a solvation probe. In partially denatured states (2-6 M urea), lower crowder concentrations (~ < 125 g/L) induced faster dynamics, while the dynamics became slower beyond 150 g/L of crowders. We propose that this apparent switch in dynamics is an evidence of a crossover from soft (enthalpic) to hard-core (entropic) interactions between the protein and crowder molecules. That soft interactions are also important for the crowders used here was further confirmed by the appreciable shift in the wavelength of the emission maximum of BADAN, in particular for PEG8000 and Ficoll 70 at concentrations where the excluded volume effect is not dominant.
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37
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Krah A, Huber RG, Bond PJ. How Ligand Binding Affects the Dynamical Transition Temperature in Proteins. Chemphyschem 2020; 21:916-926. [DOI: 10.1002/cphc.201901221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 03/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Krah
- School of Computational SciencesKorea Institute for Advanced Study 85 Hoegiro, Dongdaemun-gu Seoul 02455 Republic of Korea
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Roland G. Huber
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
| | - Peter J. Bond
- Bioinformatics InstituteAgency for Science Technology and Research (A*STAR) 30 Biopolis Str., #07-01 Matrix 138671 Singapore
- National University of SingaporeDepartment of Biological Sciences 14 Science Drive 4 Singapore 117543
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38
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Nakagawa H, Kataoka M. How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation? Biophys Physicobiol 2020; 16:213-219. [PMID: 31984174 PMCID: PMC6975894 DOI: 10.2142/biophysico.16.0_213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/29/2019] [Indexed: 12/01/2022] Open
Abstract
Incoherent neutron scattering (INS) is one of the useful experimental methods for studying protein dynamics at the pico-nanosecond timescale. At this timescale, protein dynamics is highly coupled with hydration, which is observed as protein dynamical transition (PDT). INS is very sensitive to hydrogen atomic dynamics because of the large incoherent scattering cross section of hydrogen atom, and thus, the INS of a hydrated protein provides overall dynamic information about the protein, including hydration water. Separation of hydration water dynamics is essential for understanding hydration-related protein dynamics. H2O/D2O exchange is an effective method in the context of INS experiments for observing the dynamics of protein and hydration water separately. Neutron scattering is directly related to the van Hove space-time correlation function, which can be calculated quantitatively by performing molecular dynamics (MD) simulations. Diffusion and hydrogen bond dynamics of hydration water can be analyzed by performing MD simulation. MD simulation is useful for analyzing the dynamic coupling mechanism in hydration-related protein dynamics from the viewpoint of interpreting INS data because PDT is induced by hydration. In the present work, we demonstrate the methodological advantages of the H2O/D2O exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water.
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Affiliation(s)
- Hiroshi Nakagawa
- Hierarchical Structure Research Group, Materials Science Research Center, Japan Atomic Energy Agency, Naka-gun, Ibaraki 319-1195, Japan
| | - Mikio Kataoka
- Graduate School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Naka-gun, Ibaraki, Japan
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39
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Mechanical Unfolding of Spectrin Repeats Induces Water-Molecule Ordering. Biophys J 2020; 118:1076-1089. [PMID: 32027822 DOI: 10.1016/j.bpj.2020.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 02/07/2023] Open
Abstract
Mechanical processes are involved at many stages of the development of living cells, and often external forces applied to a biomolecule result in its unfolding. Although our knowledge of the unfolding mechanisms and the magnitude of the forces involved has evolved, the role that water molecules play in the mechanical unfolding of biomolecules has not yet been fully elucidated. To this end, we investigated with steered molecular dynamics simulations the mechanical unfolding of dystrophin's spectrin repeat 1 and related the changes in the protein's structure to the ordering of the surrounding water molecules. Our results indicate that upon mechanically induced unfolding of the protein, the solvent molecules become more ordered and increase their average number of hydrogen bonds. In addition, the unfolded structures originating from mechanical pulling expose an increasing amount of the hydrophobic residues to the solvent molecules, and the uncoiled regions adapt a convex surface with a small radius of curvature. As a result, the solvent molecules reorganize around the protein's small protrusions in structurally ordered waters that are characteristic of the so-called "small-molecule regime," which allows water to maintain a high hydrogen bond count at the expense of an increased structural order. We also determined that the response of water to structural changes in the protein is localized to the specific regions of the protein that undergo unfolding. These results indicate that water plays an important role in the mechanically induced unfolding of biomolecules. Our findings may prove relevant to the ever-growing interest in understanding macromolecular crowding in living cells and their effects on protein folding, and suggest that the hydration layer may be exploited as a means for short-range allosteric communication.
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40
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Schirò G. Probing the dynamics of biological matter by elastic, quasi-elastic, and inelastic neutron scattering. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202023605001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The so-called function-structure-dynamics paradigm established that a close relationship links the way biological molecules work (function), their 3-dimensional organization (structure) and the changes of this organization in time (dynamics), which characterize biomolecules as highly dynamic objects. A typical example of protein dynamics is provided by protein reactions with substrates: equilibrium thermal fluctuations of protein structure are necessary to allow the access of substrates to the active site, where the functional reaction occurs. Neutron scattering is a powerful technique to study equilibrium protein structural dynamics. The incoherent structure factor, which is dominant in neutron scattering from biological matter, is related to the time-position self correlation function of protein/solvent nuclei. Here the basic theory of neutron scattering and the principles of the technologies used to measure it are described. Some selected applications of neutron scattering for investigating the structural dynamics of biological molecules are also reviewed.
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41
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More than a Confinement: “Soft” and “Hard” Enzyme Entrapment Modulates Biological Catalyst Function. Catalysts 2019. [DOI: 10.3390/catal9121024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Catalysis makes chemical and biochemical reactions kinetically accessible. From a technological point of view, organic, inorganic, and biochemical catalysis is relevant for several applications, from industrial synthesis to biomedical, material, and food sciences. A heterogeneous catalyst, i.e., a catalyst confined in a different phase with respect to the reagents’ phase, requires either its physical confinement in an immobilization matrix or its physical adsorption on a surface. In this review, we will focus on the immobilization of biological catalysts, i.e., enzymes, by comparing hard and soft immobilization matrices and their effect on the modulation of the catalysts’ function. Indeed, unlike smaller molecules, the catalytic activity of protein catalysts depends on their structure, conformation, local environment, and dynamics, properties that can be strongly affected by the immobilization matrices, which, therefore, not only provide physical confinement, but also modulate catalysis.
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42
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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43
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Golub M, Moldenhauer M, Schmitt FJ, Lohstroh W, Maksimov EG, Friedrich T, Pieper J. Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering. J Phys Chem B 2019; 123:9536-9545. [PMID: 31550157 DOI: 10.1021/acs.jpcb.9b05073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Orange carotenoid proteins (OCPs), which are protecting cyanobacterial light-harvesting antennae from photodamage, undergo a pronounced structural change upon light absorption. In addition, the active state is anticipated to boost a significantly higher molecular flexibility similar to a "molten globule" state. Here, we used quasielastic neutron scattering to directly characterize the vibrational and conformational molecular dynamics of OCP in its ground and active states, respectively, on the picosecond time scale. At a temperature of 100 K, we observe mainly (vibronic) inelastic features with peak energies at 5 and 6 meV (40 and 48 cm-1, respectively). At physiological temperatures, however, two (Lorentzian) quasielastic components represent localized protein motions, that is, stochastic structural fluctuations of protein side chains between various conformational substates of the protein. Global diffusion of OCP is not observed on the given time scale. The slower Lorentzian component is affected by illumination and can be well-characterized by a jump-diffusion model. While the jump diffusion constant D is (2.82 ± 0.01) × 10-5 cm2/s at 300 K in the ground state, it is increased by ∼20% to (3.48 ± 0.01) × 10-5 cm2/s in the active state, revealing a strong enhancement of molecular mobility. The increased mobility is also reflected in the average atomic mean square displacement ⟨u2⟩; we determine a ⟨u2⟩ of 1.47 ± 0.05 Å in the ground state, but 1.86 ± 0.05 Å in the active state (at 300 K). This effect is assigned to two factors: (i) the elongated structure of the active state with two widely separated protein domains is characterized by a larger number of surface residues with a concomitantly higher degree of motional freedom and (ii) a larger number of hydration water molecules bound at the surface of the protein. We thus conclude that the active state of the orange carotenoid protein displays an enhanced conformational dynamics. The higher degree of flexibility may provide additional channels for nonradiative decay so that harmful excess energy can be more efficiently converted to heat.
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Affiliation(s)
- Maksym Golub
- Institute of Physics , University of Tartu , 50411 Tartu , Estonia
| | - Marcus Moldenhauer
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum , Technische Universität München , Garching , Germany
| | - Eugene G Maksimov
- Department of Biophysics , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Thomas Friedrich
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Jörg Pieper
- Institute of Physics , University of Tartu , 50411 Tartu , Estonia
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Bachler J, Handle PH, Giovambattista N, Loerting T. Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations. Phys Chem Chem Phys 2019; 21:23238-23268. [PMID: 31556899 DOI: 10.1039/c9cp02953b] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.
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Affiliation(s)
- Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria.
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Iorio A, Camisasca G, Rovere M, Gallo P. Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network. J Chem Phys 2019; 151:044507. [PMID: 31370561 DOI: 10.1063/1.5108579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.
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Affiliation(s)
- A Iorio
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - G Camisasca
- Department of Physics, AlbaNova University Center, Stockholm University, S-106 91 Stockholm, Sweden
| | - M Rovere
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
| | - P Gallo
- Dipartimento di Matematica e Fisica, Università Roma Tre, Via della Vasca Navale 84, 00146 Rome, Italy
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46
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Wohlfromm T, Vogel M. On the coupling of protein and water dynamics in confinement: Spatially resolved molecular dynamics simulation studies. J Chem Phys 2019; 150:245101. [DOI: 10.1063/1.5097777] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Timothy Wohlfromm
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Michael Vogel
- Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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47
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Salvi N, Abyzov A, Blackledge M. Solvent-dependent segmental dynamics in intrinsically disordered proteins. SCIENCE ADVANCES 2019; 5:eaax2348. [PMID: 31259246 PMCID: PMC6598773 DOI: 10.1126/sciadv.aax2348] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/04/2023]
Abstract
Protein and water dynamics have a synergistic relationship, which is particularly important for intrinsically disordered proteins (IDPs), although the details of this coupling remain poorly understood. Here, we combine temperature-dependent molecular dynamics simulations using different water models with extensive nuclear magnetic resonance (NMR) relaxation to examine the importance of distinct modes of solvent and solute motion for the accurate reproduction of site-specific dynamics in IDPs. We find that water dynamics play a key role in motional processes internal to "segments" of IDPs, stretches of primary sequence that share dynamic properties and behave as discrete dynamic units. We identify a relationship between the time scales of intrasegment dynamics and the lifetime of hydrogen bonds in bulk water. Correct description of these motions is essential for accurate reproduction of protein relaxation. Our findings open important perspectives for understanding the role of hydration water on the behavior and function of IDPs in solution.
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48
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Olsson C, Genheden S, García Sakai V, Swenson J. Mechanism of Trehalose-Induced Protein Stabilization from Neutron Scattering and Modeling. J Phys Chem B 2019; 123:3679-3687. [PMID: 30964287 DOI: 10.1021/acs.jpcb.9b01856] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sugar molecule trehalose has been proven to be an excellent stabilizing cosolute for the preservation of biological materials. However, the stabilizing mechanism of trehalose has been much debated during the previous decades, and it is still not fully understood, partly because it has not been completely established how trehalose molecules structure around proteins. Here, we present a molecular model of a protein-water-trehalose system, based on neutron scattering results obtained from neutron diffraction, quasielastic neutron scattering, and different computer modeling techniques. The structural data clearly show how the proteins are preferentially hydrated, and analysis of the dynamical properties show that the protein residues are slowed down because of reduced dynamics of the protein hydration shell, rather than because of direct trehalose-protein interactions. These findings, thereby, strongly support previous models related to the preferential hydration model and contradict other models based on water replacement at the protein surface. Furthermore, the results are important for understanding the specific role of trehalose in biological stabilization and, more generally, for providing a likely mechanism of how cosolutes affect the dynamics of proteins.
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Affiliation(s)
- Christoffer Olsson
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
| | - Samuel Genheden
- Deparment of Chemistry and Molecular Biology , University of Gothenburg , Box 462, SE-405 30 Göteborg , Sweden
| | - Victoria García Sakai
- ISIS Facility, STFC Rutherford Appleton Laboratory , Harwell Campus , Didcot , OX11 0QX Oxfordshire , U.K
| | - Jan Swenson
- Department of Physics , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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Hirakawa K, Koike K, Kanawaku Y, Moriyama T, Sato N, Suzuki T, Furihata K, Ohno Y. Short-time Fourier Transform of Free Induction Decays for the Analysis of Serum Using Proton Nuclear Magnetic Resonance. J Oleo Sci 2019; 68:369-378. [PMID: 30867391 DOI: 10.5650/jos.ess18212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proton nuclear magnetic resonance (NMR) is useful for the analysis of biological samples such as serum. Free induction decays (FIDs) are NMR signals that follow a radio-frequency pulse applied at the resonance frequency. Short-time Fourier transform (STFT) is a basic method for time-frequency analyses. The purpose of this study was to ascertain whether the STFT of FIDs enables the sensitive detection of changes and differences in serum properties. FIDs were obtained from serum collected from young, healthy, male volunteers ≤ 40 years of age and seniors ≥ 65 years of age. Temporal changes in the instantaneous amplitudes for the time-domain analysis, fast Fourier transform for frequency-domain analysis, and STFT were applied to the FIDs. The STFT-based spectrogram represented the complex frequency components that changed dynamically over time, indicating that the spectrogram enabled the visualization of the features of an FID. Furthermore, the results of a partial least-squares discriminant analysis demonstrated that the STFT was superior to the other two methods for discriminating between serum from younger and older subjects. In conclusion, the STFT of FIDs obtained from proton NMR measurements was useful for evaluating similarities and dissimilarities in the FIDs obtained from serum samples.
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Affiliation(s)
- Keiko Hirakawa
- Research Laboratory for Magnetic Resonance, Nippon Medical School
| | - Kaoru Koike
- Department of Primary Care and Emergency Medicine, Kyoto University, Graduate School of Medicine
| | | | - Tsuyoshi Moriyama
- Department of Media and Image Technology, Tokyo Polytechnic University
| | - Norio Sato
- Department of Primary Care and Emergency Medicine, Kyoto University, Graduate School of Medicine
| | - Takao Suzuki
- Department of Primary Care and Emergency Medicine, Kyoto University, Graduate School of Medicine
| | | | - Youkichi Ohno
- Research Laboratory for Magnetic Resonance, Nippon Medical School.,Department of Legal Medicine, Nippon Medical School
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50
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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