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König B, Pezzotti S, Ramos S, Schwaab G, Havenith M. Real-time measure of solvation free energy changes upon liquid-liquid phase separation of α-elastin. Biophys J 2024; 123:1367-1375. [PMID: 37515326 PMCID: PMC11163292 DOI: 10.1016/j.bpj.2023.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Biological condensates are known to retain a large fraction of water to remain in a liquid and reversible state. Local solvation contributions from water hydrating hydrophilic and hydrophobic protein surfaces were proposed to play a prominent role for the formation of condensates through liquid-liquid phase separation (LLPS). However, although the total free energy is accessible by calorimetry, the partial solvent contributions to the free energy changes upon LLPS remained experimentally inaccessible so far. Here, we show that the recently developed THz calorimetry approach allows to quantify local hydration enthalpy and entropy changes upon LLPS of α-elastin in real time, directly from experimental THz spectroscopy data. We find that hydrophobic solvation dominates the entropic solvation term, whereas hydrophilic solvation mainly contributes to the enthalpy. Both terms are in the order of hundreds of kJ/mol, which is more than one order of magnitude larger than the total free energy changes at play during LLPS. However, since we show that entropy/enthalpy mostly compensates, a small entropy/enthalpy imbalance is sufficient to tune LLPS. Theoretically, a balance was proposed before. Here we present experimental evidence based on our spectroscopic approach. We finally show that LLPS can be steered by inducing small changes of solvation entropy/enthalpy compensation via concentration or temperature in α-elastin.
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Affiliation(s)
- Benedikt König
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Sashary Ramos
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany.
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2
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Abstract
Terahertz time-domain spectroscopy (THz-TDS) is a non-invasive, non-contact and label-free technique for biological and chemical sensing as THz-spectra are less energetic and lie in the characteristic vibration frequency regime of proteins and DNA molecules. However, THz-TDS is less sensitive for the detection of micro-organisms of size equal to or less than λ/100 (where, λ is the wavelength of the incident THz wave), and molecules in extremely low concentration solutions (like, a few femtomolar). After successful high-throughput fabrication of nanostructures, nanoantennas were found to be indispensable in enhancing the sensitivity of conventional THz-TDS. These nanostructures lead to strong THz field enhancement when in resonance with the absorption spectrum of absorptive molecules, causing significant changes in the magnitude of the transmission spectrum, therefore, enhancing the sensitivity and allowing the detection of molecules and biomaterials in extremely low concentration solutions. Herein, we review the recent developments in ultra-sensitive and selective nanogap biosensors. We have also provided an in-depth review of various high-throughput nanofabrication techniques. We also discussed the physics behind the field enhancements in the sub-skin depth as well as sub-nanometer sized nanogaps. We introduce finite-difference time-domain (FDTD) and molecular dynamics (MD) simulation tools to study THz biomolecular interactions. Finally, we provide a comprehensive account of nanoantenna enhanced sensing of viruses (like, H1N1) and biomolecules such as artificial sweeteners which are addictive and carcinogenic.
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Affiliation(s)
- Subham Adak
- Department of Physics, Birla Institute of Technology, Mesra, Ranchi - 835215, Jharkhand, India.
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3
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Brühl E, Buckup T, Motzkus M. Experimental and numerical investigation of a phase-only control mechanism in the linear intensity regime. J Chem Phys 2018; 148:214310. [DOI: 10.1063/1.5029805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Elisabeth Brühl
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Tiago Buckup
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Marcus Motzkus
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, D-69120 Heidelberg, Germany
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4
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Han Y, Ling S, Qi Z, Shao Z, Chen X. Application of far-infrared spectroscopy to the structural identification of protein materials. Phys Chem Chem Phys 2018; 20:11643-11648. [DOI: 10.1039/c8cp00802g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Far-IR spectroscopy was applied to monitor the structure of two types of silk fibroins and the results indicate that they both show several sharp characteristic peaks, which are totally different from those of globular proteins.
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Affiliation(s)
- Yanchen Han
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University
- Shanghai
- People's Republic of China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University
- Shanghai
- People's Republic of China
| | - Zeming Qi
- National Synchrotron Radiation Laboratory, University of Science and Technology of China
- Hefei
- People's Republic of China
| | - Zhengzhong Shao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University
- Shanghai
- People's Republic of China
| | - Xin Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University
- Shanghai
- People's Republic of China
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5
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Cote Y, Nominé Y, Ramirez J, Hellwig P, Stote RH. Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations. Biophys J 2017. [PMID: 28636914 DOI: 10.1016/j.bpj.2017.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained. MD simulations were used to determine the most representative structure of each form and these were used to compute their respective IR spectra by normal mode analysis. Far-UV circular dichroism spectroscopy was used to confirm the secondary structure content and the stability through temperature-dependent studies. Both the experimental and calculated far-IR spectra showed a red shift of the low-frequency peaks upon peptide binding. The calculations show that this is coincident with an increased number of hydrogen bonds formed as the peptide augments the protein β-sheet. We further identified the contribution of surface-bound water molecules to bands in the far-IR and, through the calculations, identified potential pathways for allosteric communication. Together, these results demonstrate the utility of combining far-IR experiments and MD studies to study peptide binding by proteins.
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Affiliation(s)
- Yoann Cote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France
| | - Yves Nominé
- Équipe Labellisée Ligue Contre le Cancer, Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France
| | - Juan Ramirez
- Equipe Oncoprotéines, Ecole Supérieure de Biotechnologie de Strasbourg, Biotechnologie et Signalisation Cellulaire, UMR 7242, CNRS, Université de Strasbourg, Illkirch, France
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 UMR 7104 CNRS, Université de Strasbourg, Illkirch, France.
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6
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Balčytis A, Ryu M, Wang X, Novelli F, Seniutinas G, Du S, Wang X, Li J, Davis J, Appadoo D, Morikawa J, Juodkazis S. Silk: Optical Properties over 12.6 Octaves THz-IR-Visible-UV Range. MATERIALS (BASEL, SWITZERLAND) 2017; 10:E356. [PMID: 28772716 PMCID: PMC5507002 DOI: 10.3390/ma10040356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/02/2017] [Accepted: 03/23/2017] [Indexed: 12/04/2022]
Abstract
Domestic (Bombyx mori) and wild (Antheraea pernyi) silk fibers were characterised over a wide spectral range from THz 8 cm -1 ( λ = 1.25 mm, f = 0.24 THz) to deep-UV 50 × 10 3 cm - 1 ( λ = 200 nm, f = 1500 THz) wavelengths or over a 12.6 octave frequency range. Spectral features at β-sheet, α-coil and amorphous fibroin were analysed at different spectral ranges. Single fiber cross sections at mid-IR were used to determine spatial distribution of different silk constituents and revealed an α-coil rich core and more broadly spread β-sheets in natural silk fibers obtained from wild Antheraea pernyi moths. Low energy T-ray bands at 243 and 229 cm -1 were observed in crystalline fibers of domestic and wild silk fibers, respectively, and showed no spectral shift down to 78 K temperature. A distinct 20±4 cm-1 band was observed in the crystalline Antheraea pernyi silk fibers. Systematic analysis and assignment of the observed spectral bands is presented. Water solubility and biodegradability of silk, required for bio-medical and sensor applications, are directly inferred from specific spectral bands.
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Affiliation(s)
- Armandas Balčytis
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
- Department of Laser Technologies, Center for Physical Sciences and Technology, Savanoriu Ave. 231, LT-02300 Vilnius, Lithuania.
- These authors contributed equally to this work..
| | - Meguya Ryu
- Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.
- These authors contributed equally to this work..
| | - Xuewen Wang
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
- These authors contributed equally to this work..
| | - Fabio Novelli
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
- Current address: Ruhr-University Bochum, 44801 Bochum, Germany..
| | - Gediminas Seniutinas
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
- Current address: Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland..
| | - Shan Du
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia.
| | - Xungai Wang
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia.
| | - Jingliang Li
- Australian Future Fibres Research and Innovation Centre, Institute for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia.
| | - Jeffrey Davis
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
| | - Dominique Appadoo
- Australian Synchrotron, Blackburn Road, Clayton, VIC 3168, Australia.
| | - Junko Morikawa
- Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.
| | - Saulius Juodkazis
- School of Science, Faculty of Engineering and Industrial Sciences, Swinburne University of Technology, Hawthorn, VIC 3122, Australia.
- Melbourne Centre for Nanofabrication, the Victorian Node of the Australian National Fabrication Facility, 151 Wellington Rd., Clayton, VIC 3168, Australia.
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7
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Yatsyna V, Bakker DJ, Feifel R, Rijs AM, Zhaunerchyk V. Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide. J Chem Phys 2017; 145:104309. [PMID: 27634262 DOI: 10.1063/1.4962360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.
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Affiliation(s)
- Vasyl Yatsyna
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Daniël J Bakker
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Raimund Feifel
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anouk M Rijs
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernoovield 7-c, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
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8
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Karain W. THz frequency spectrum of protein-solvent interaction energy using a recurrence plot-based Wiener-Khinchin method. Proteins 2016; 84:1549-57. [PMID: 27357803 DOI: 10.1002/prot.25097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/05/2016] [Accepted: 06/28/2016] [Indexed: 11/10/2022]
Abstract
The dynamics of a protein and the water surrounding it are coupled via nonbonded energy interactions. This coupling can exhibit a complex, nonlinear, and nonstationary nature. The THz frequency spectrum for this interaction energy characterizes both the vibration spectrum of the water hydrogen bond network, and the frequency range of large amplitude modes of proteins. We use a Recurrence Plot based Wiener-Khinchin method RPWK to calculate this spectrum, and the results are compared to those determined using the classical auto-covariance-based Wiener-Khinchin method WK. The frequency spectra for the total nonbonded interaction energy extracted from molecular dynamics simulations between the β-Lactamase Inhibitory Protein BLIP, and water molecules within a 10 Å distance from the protein surface, are calculated at 150, 200, 250, and 310 K, respectively. Similar calculations are also performed for the nonbonded interaction energy between the residues 49ASP, 53TYR, and 142PHE in BLIP, with water molecules within 10 Å from each residue respectively at 150, 200, 250, and 310 K. A comparison of the results shows that RPWK performs better than WK, and is able to detect some frequency data points that WK fails to detect. This points to the importance of using methods capable of taking the complex nature of the protein-solvent energy landscape into consideration, and not to rely on standard linear methods. In general, RPWK can be a valuable addition to the analysis tools for protein molecular dynamics simulations. Proteins 2016; 84:1549-1557. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wael Karain
- Department of Physics, Birzeit University, Birzeit, Palestine.
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9
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Raphael AP, Crichton ML, Falconer RJ, Meliga S, Chen X, Fernando GJP, Huang H, Kendall MAF. Formulations for microprojection/microneedle vaccine delivery: Structure, strength and release profiles. J Control Release 2016; 225:40-52. [PMID: 26795684 DOI: 10.1016/j.jconrel.2016.01.027] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/25/2015] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
To develop novel methods for vaccine delivery, the skin is viewed as a high potential target, due to the abundance of immune cells that reside therein. One method, the use of dissolving microneedle technologies, has the potential to achieve this, with a range of formulations now being employed. Within this paper we assemble a range of methods (including FT-FIR using synchrotron radiation, nanoindentation and skin delivery assays) to systematically examine the effect of key bulking agents/excipients - sugars/polyols - on the material form, structure, strength, failure properties, diffusion and dissolution for dissolving microdevices. We investigated concentrations of mannitol, sucrose, trehalose and sorbitol from 1:1 to 30:1 with carboxymethylcellulose (CMC), although mannitol did not form our micro-structures so was discounted early in the study. The other formulations showed a variety of crystalline (sorbitol) and amorphous (sucrose, trehalose) structures, when investigated using Fourier transform far infra-red (FT-FIR) with synchrotron radiation. The crystalline structures had a higher elastic modulus than the amorphous formulations (8-12GPa compared to 0.05-11GPa), with sorbitol formulations showing a bimodal distribution of results including both amorphous and crystalline behaviour. In skin, diffusion properties were similar among all formulations with dissolution occurring within 5s for our small projection array structures (~100μm in length). Overall, slight variations in formulation can significantly change the ability of our projections to perform their required function, making the choice of bulking/vaccine stabilising agents of great importance for these devices.
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Affiliation(s)
- Anthony P Raphael
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia
| | - Michael L Crichton
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Australia
| | - Robert J Falconer
- University of Sheffield, Department of Chemical & Biological Engineering, ChELSI Institute, Sheffield S1 3JD, England, United Kingdom
| | - Stefano Meliga
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia
| | - Xianfeng Chen
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia
| | - Germain J P Fernando
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia
| | - Han Huang
- The University of Queensland, School of Mechanical and Mining Engineering, QLD 4072, Australia
| | - Mark A F Kendall
- The University of Queensland, Delivery of Drugs and Genes Group (D(2)G(2)), Australian Institute for Bioengineering and Nanotechnology, QLD 4072, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of Queensland, Australia; The University of Queensland, Faculty of Medicine and Biomedical Sciences, Royal Brisbane and Women's Hospital, Herston, Queensland 4006, Australia.
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10
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Woods KN, Pfeffer J. Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes. Mol Biol Evol 2016; 33:40-61. [PMID: 26337549 PMCID: PMC4693973 DOI: 10.1093/molbev/msv178] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function.
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11
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Wallace VP, Ferachou D, Ke P, Day K, Uddin S, Casas-Finet J, Van Der Walle CF, Falconer RJ, Zeitler JA. Modulation of the Hydration Water Around Monoclonal Antibodies on Addition of Excipients Detected by Terahertz Time-Domain Spectroscopy. J Pharm Sci 2015; 104:4025-4033. [DOI: 10.1002/jps.24630] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/25/2015] [Accepted: 08/04/2015] [Indexed: 12/25/2022]
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12
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Zhang M, Wei D, Tang M, Shi C, Cui HL, Du C. Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Far-infrared spectroscopy of salt penetration into a collagen fiber scaffold. J Biol Phys 2015; 41:293-301. [PMID: 25764184 DOI: 10.1007/s10867-015-9379-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 01/19/2015] [Indexed: 10/23/2022] Open
Abstract
We employed far-infrared spectroscopy to observe the amount of salt that penetrates into collagen fiber masses. The absorption properties of collagen sheets prepared from tilapia skin, bovine skin, rat tail, and sea cucumber dermis were measured using a transmission Fourier transform spectrometer in a band from approximately 100 to 700 cm(-1). We confirmed that the absorbance spectra of the four types of dried collagen sheet show good agreement, even though the amino acid compositions differed. The absorbance peaks observed in the band corresponded to collective vibrations of plural functional groups such as methylene and imino groups in collagen. When salt solution was added to the collagen sheets and then dried, the spectral shapes of the sheets at approximately 166 cm(-1) were clearly different from those of the plain collagen sheets. The differential absorbance between wavenumbers 166 cm(-1) and 250 cm(-1) sensitively reflected the difference between higher-order structures, and the salt diffusion (crystallization) depended on the collagen fiber condition. From these results, we consider that spectral changes can be used for the numerical evaluation of salt penetration into a collagen fiber scaffold.
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14
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Sushko O, Dubrovka R, Donnan RS. Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected. J Chem Phys 2015; 142:055101. [DOI: 10.1063/1.4907271] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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15
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Liem SY, Popelier PLA. The hydration of serine: multipole moments versus point charges. Phys Chem Chem Phys 2014; 16:4122-34. [PMID: 24448691 DOI: 10.1039/c3cp54723j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Next-generation force fields must incorporate improved electrostatic potentials in order to increase the reliability of their predictions. A crucial decision toward this goal is to abandon point charges in favour of multipole moments centered on nuclear sites. Here we compare the geometries generated by quantum topological multipole moments with those generated by four popular point charge models (TAFF, OPLS-AA, MMFF94x and PFROSST) for a hydrated serine. A main feature of this study is the dual comparison made, both at static level (geometry optimisation via energy minimisation) and at dynamic level (via molecular dynamics and radial/spatial distribution function analysis). At static level, multipolar electrostatics best reproduces the ab initio reference geometry. At dynamic level, multipolar electrostatics produces more structure than point charge electrostatics does, over the whole range. From our previous work on liquid water [Int. J. Quantum. Chem., 2004, 99, 685], where agreement with experiment only occurs when using multipole moments, we deduce that our predictions for hydrated serine will also be closer to experiment when using multipolar electrostatics. The spatial distribution function shows that only multipolar electrostatics shows pronounced structure at long range. Even at short range there are many regions where waters appear in the system governed by multipolar electrostatics but not in that governed by point charges.
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Affiliation(s)
- Steven Y Liem
- Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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16
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Woods KN. The glassy state of crambin and the THz time scale protein-solvent fluctuations possibly related to protein function. BMC BIOPHYSICS 2014; 7:8. [PMID: 25184036 PMCID: PMC4143578 DOI: 10.1186/s13628-014-0008-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/04/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND THz experiments have been used to characterize the picosecond time scale fluctuations taking place in the model, globular protein crambin. RESULTS Using both hydration and temperature as an experimental parameter, we have identified collective fluctuations (<= 200 cm(-1)) in the protein. Observation of the protein dynamics in the THz spectrum from both below and above the glass transition temperature (Tg) has provided unique insight into the microscopic interactions and modes that permit the solvent to effectively couple to the protein thermal fluctuations. CONCLUSIONS Our findings suggest that the solvent dynamics on the picosecond time scale not only contribute to protein flexibility but may also delineate the types of fluctuations that are able to form within the protein structure.
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Affiliation(s)
- Kristina N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh 15213, PA, USA
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Woods KN. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. SOFT MATTER 2014; 10:4387-4402. [PMID: 24801988 DOI: 10.1039/c3sm53229a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this investigation we use THz time-scale spectroscopy to conduct an initial set of studies on myoglobin with the aim of providing further insight into the global, collective thermal fluctuations in the protein that have been hypothesized to play a prominent role in the dynamic formation of transient ligand channels as well as in shaping the molecular level basis for ligand discrimination. Using the two ligands O2 and CO, we have determined that the perturbation from the heme-ligand complex has a strong influence on the characteristics of the myoglobin collective dynamics that are excited upon binding. Further, the differences detected in the collective protein motions in Mb-O2 compared with those in Mb-CO appear to be intimately tied with the pathways of long-range allosteric communication in the protein, which ultimately determine the trajectories selected by the respective ligands on the path to and from the heme-binding cavity.
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Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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18
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Sun J, Niehues G, Forbert H, Decka D, Schwaab G, Marx D, Havenith M. Understanding THz Spectra of Aqueous Solutions: Glycine in Light and Heavy Water. J Am Chem Soc 2014; 136:5031-8. [DOI: 10.1021/ja4129857] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jian Sun
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Gudrun Niehues
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Harald Forbert
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Dominique Decka
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Theoretische Chemie and ‡Lehrstuhl für Physikalische
Chemie II, Ruhr−Universität Bochum, 44780 Bochum, Germany
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19
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Bye JW, Meliga S, Ferachou D, Cinque G, Zeitler JA, Falconer RJ. Analysis of the Hydration Water around Bovine Serum Albumin Using Terahertz Coherent Synchrotron Radiation. J Phys Chem A 2013; 118:83-8. [DOI: 10.1021/jp407410g] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jordan W. Bye
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield S1 3JD, England
| | - Stefano Meliga
- Australian Institute
for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Denis Ferachou
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB2 3RA, England
| | | | - J. Axel Zeitler
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge CB2 3RA, England
| | - Robert J. Falconer
- Department of Chemical & Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield S1 3JD, England
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Sushko O, Dubrovka R, Donnan RS. Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure. J Phys Chem B 2013; 117:16486-92. [DOI: 10.1021/jp407580y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oleksandr Sushko
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Rostyslav Dubrovka
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Robert S. Donnan
- School
of Electronic Engineering
and Computer Science, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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21
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Prediction of vapor–liquid equilibria of alcohol+hydrocarbon systems by 1H NMR spectroscopy. Chem Eng Sci 2012. [DOI: 10.1016/j.ces.2012.03.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Lipps F, Levy S, Markelz AG. Hydration and temperature interdependence of protein picosecond dynamics. Phys Chem Chem Phys 2012; 14:6375-81. [DOI: 10.1039/c2cp23760a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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