1
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Shirley JC, Baiz CR. MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe. J Phys Chem B 2024; 128:5310-5319. [PMID: 38806061 DOI: 10.1021/acs.jpcb.4c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.
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Affiliation(s)
- Joseph C Shirley
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
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2
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Felsted RG, Graham TR, Zhao Y, Bazak JD, Nienhuis ET, Pauzauskie PJ, Joly AG, Pearce CI, Wang Z, Rosso KM. Anionic Effects on Concentrated Aqueous Lithium Ion Dynamics. J Phys Chem Lett 2024:5076-5087. [PMID: 38708887 DOI: 10.1021/acs.jpclett.4c00585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The dynamics, orientational anisotropy, diffusivity, viscosity, and density were measured for concentrated lithium salt solutions, including lithium chloride (LiCl), lithium bromide (LiBr), lithium nitrite (LiNO2), and lithium nitrate (LiNO3), with methyl thiocyanate as an infrared vibrational probe molecule, using two-dimensional infrared spectroscopy (2D IR), nuclear magnetic resonance (NMR) spectroscopy, and viscometry. The 2D IR, NMR, and viscosity results show that LiNO2 exhibits longer correlation times, lower diffusivity, and nearly 4 times greater viscosity compared to those of the other lithium salt solutions of the same concentration, suggesting that nitrite anions may strongly facilitate structure formation via strengthening water-ion network interactions, directly impacting bulk solution properties at sufficiently high concentrations. Additionally, the LiNO2 and LiNO3 solutions show significantly weakened chemical interactions between the lithium cations and the methyl thiocyanate when compared with those of the lithium halide salts.
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Affiliation(s)
- Robert G Felsted
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Trent R Graham
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yatong Zhao
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - J David Bazak
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Emily T Nienhuis
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter J Pauzauskie
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Materials Science and Engineering Department, University of Washington, Seattle, Washington 98195, United States
| | - Alan G Joly
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Carolyn I Pearce
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington 99164, United States
| | - Zheming Wang
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kevin M Rosso
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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3
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Miyagawa A, Ueda Y, Nakatani K. Molecular crowding effect in Hantzch pyridine synthesis in polyethylene glycol aqueous solution. Phys Chem Chem Phys 2024; 26:5615-5620. [PMID: 38288480 DOI: 10.1039/d3cp06104c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
In a molecular crowding environment, the kinetics and thermodynamics differ from those in a diluted solution. Although the molecular crowding effect has been extensively investigated, its fundamental kinetics and thermodynamics remain unclear. In this study, we investigated the change in the rate constant (k) of the Hantzch pyridine reaction in a molecular crowding environment using polyethylene glycol (PEG). While the k value increased to a PEG concentration (CPEG) of 10 vol%, a decreasing trend was observed for CPEG > 20 vol%. This intriguing behavior was analyzed based on the increase in reactant activity due to volume exclusion and the decrease in water activity due to osmotic pressure. Volume exclusion and osmotic pressure had opposing effects on the reaction, which were positive for volume exclusion and negative for osmotic pressure. We found that k decreased when the negative effect of the osmotic pressure surpassed the volume exclusion effect.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuyuki Ueda
- Institute of Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kiyoharu Nakatani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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4
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Majumdar S, Rastogi H, Chowdhury PK. Bridging Soft Interaction and Excluded Volume in Crowded Milieu through Subtle Protein Dynamics. J Phys Chem B 2024; 128:716-730. [PMID: 38226816 DOI: 10.1021/acs.jpcb.3c07266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The impact of macromolecular crowding on biological macromolecules has been elucidated through the excluded volume phenomenon and soft interactions. However, it has often been difficult to provide a clear demarcation between the two regions. Here, using temperature-dependent dynamics (local and global) of the multidomain protein human serum albumin (HSA) in the presence of commonly used synthetic crowders (Dextran 40, PEG 8, Ficoll 70, and Dextran 70), we have shown the presence of a transition that serves as a bridge between the soft and hard regimes. The bridging region is independent of the crowder identity and displays no apparent correlation with the critical overlap concentration of the polymeric crowding agents. Moreover, the dynamics of domains I and II and the protein gating motion respond differently, thereby bringing to the fore the asymmetry underlying the crowder influence on HSA. In addition, solvent-coupled and decoupled protein motions indicate the heterogeneity of the dynamic landscape in the crowded milieu. We also propose an intriguing correlation between protein stability and dynamics, with increased global stability being accompanied by eased local domain motion.
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Affiliation(s)
- Shubhangi Majumdar
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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5
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Lorenz-Ochoa KA, Baiz CR. Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates. J Am Chem Soc 2023; 145:27800-27809. [PMID: 38061016 DOI: 10.1021/jacs.3c10862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.
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Affiliation(s)
- Keegan A Lorenz-Ochoa
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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6
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Krevert C, Chavez D, Chatterjee S, Stelzl LS, Pütz S, Roeters SJ, Rudzinski JF, Fawzi NL, Girard M, Parekh SH, Hunger J. Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 2023; 14:11224-11234. [PMID: 38056002 PMCID: PMC10726384 DOI: 10.1021/acs.jpclett.3c02790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.
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Affiliation(s)
- Carola
S. Krevert
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Chavez
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sayantan Chatterjee
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Lukas S. Stelzl
- KOMET 1,
Institute of Physics, Johannes Gutenberg
University, Staudingerweg 7, 55099 Mainz, Germany
- Faculty of
Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), Ackermannweg 2, 55128 Mainz, Germany
| | - Sabine Pütz
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department
of Anatomy and Neurosciences, Amsterdam
UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Joseph F. Rudzinski
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- IRIS
Adlershof, Humboldt-Universität zu
Berlin, Zum Großen
Windkanal 2, 12489 Berlin, Germany
| | - Nicolas L. Fawzi
- Department
of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Martin Girard
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Johannes Hunger
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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7
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Xu C, Fracassi A, Baryiames CP, Bhattacharya A, Devaraj NK, Baiz CR. Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments. Chemphyschem 2023; 24:e202300404. [PMID: 37486881 DOI: 10.1002/cphc.202300404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.
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Affiliation(s)
- Cong Xu
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Alessandro Fracassi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Christopher P Baryiames
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
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8
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Kriegel M, Muller YA. De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO. Sci Rep 2023; 13:16680. [PMID: 37794104 PMCID: PMC10550942 DOI: 10.1038/s41598-023-43659-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
By mediating interatomic interactions, water molecules play a major role in protein-protein, protein-DNA and protein-ligand interfaces, significantly affecting affinity and specificity. This notwithstanding, explicit water molecules are usually not considered in protein design software because of high computational costs. To challenge this situation, we analyzed the binding characteristics of 60,000 waters from high resolution crystal structures and used the observed parameters to implement the prediction of water molecules in the protein design and side chain-packing software MUMBO. To reduce the complexity of the problem, we incorporated water molecules through the solvation of rotamer pairs instead of relying on solvated rotamer libraries. Our validation demonstrates the potential of our algorithm by achieving recovery rates of 67% for bridging water molecules and up to 86% for fully coordinated waters. The efficacy of our algorithm is highlighted further by the prediction of 3 different proteinligand complexes. Here, 91% of water-mediated interactions between protein and ligand are correctly predicted. These results suggest that the new algorithm could prove highly beneficial for structure-based protein design, particularly for the optimization of ligand-binding pockets or protein-protein interfaces.
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Affiliation(s)
- Mark Kriegel
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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9
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Shmool TA, Martin LK, Jirkas A, Matthews RP, Constantinou AP, Vadukul DM, Georgiou TK, Aprile FA, Hallett JP. Unveiling the Rational Development of Stimuli-Responsive Silk Fibroin-Based Ionogel Formulations. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:5798-5808. [PMID: 37576585 PMCID: PMC10413859 DOI: 10.1021/acs.chemmater.3c00303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/20/2023] [Indexed: 08/15/2023]
Abstract
We present an approach for the rational development of stimuli-responsive ionogels which can be formulated for precise control of multiple unique ionogel features and fill niche pharmaceutical applications. Ionogels are captivating materials, exhibiting self-healing characteristics, tunable mechanical and structural properties, high thermal stability, and electroconductivity. However, the majority of ionogels developed require complex chemistry, exhibit high viscosity, poor biocompatibility, and low biodegradability. In our work, we overcome these limitations. We employ a facile production process and strategically integrate silk fibroin, the biocompatible ionic liquids (ILs) choline acetate ([Cho][OAc]), choline dihydrogen phosphate ([Cho][DHP]), and choline chloride ([Cho][Cl]), traditional pharmaceutical excipients, and the model antiepileptic drug phenobarbital. In the absence of ILs, we failed to observe gel formation; yet in the presence of ILs, thermoresponsive ionogels formed. Systems were assessed via visual tests, transmission electron microscopy, confocal reflection microscopy, dynamic light scattering, zeta potential and rheology measurements. We formed diverse ionogels of strengths ranging between 18 and 642 Pa. Under 25 °C storage, formulations containing polyvinylpyrrolidone (PVP) showed an ionogel formation period ranging over 14 days, increasing in the order of [Cho][DHP], [Cho][OAc], and [Cho][Cl]. Formulations lacking PVP showed an ionogel formation period ranging over 32 days, increasing in the order of [Cho][OAc], [Cho][DHP] and [Cho][Cl]. By heating from 25 to 60 °C, immediately following preparation, thermoresponsive ionogels formed below 41 °C in the absence of PVP. Based on our experimental results and density functional theory calculations, we attribute ionogel formation to macromolecular crowding and confinement effects, further enhanced upon PVP inclusion. Holistically, applying our rational development strategy enables the production of ionogels of tunable physicochemical and rheological properties, enhanced drug solubility, and structural and energetic stability. We believe our rational development approach will advance the design of biomaterials and smart platforms for diverse drug delivery applications.
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Affiliation(s)
- Talia A. Shmool
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Laura K. Martin
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K.
| | - Andreas Jirkas
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Richard P. Matthews
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
- Department
of Bioscience, School of Health, Sports and Bioscience, University of East London, Stratford, London E15 4LZ, U.K.
| | - Anna P. Constantinou
- Department
of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Devkee M. Vadukul
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Theoni K. Georgiou
- Department
of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K.
| | - Francesco A. Aprile
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
- Institute
of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, U.K.
| | - Jason P. Hallett
- Department
of Chemical Engineering, Imperial College
London, South Kensington Campus, London SW7 2AZ, U.K.
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10
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Fresch E, Collini E. The Role of H-Bonds in the Excited-State Properties of Multichromophoric Systems: Static and Dynamic Aspects. Molecules 2023; 28:molecules28083553. [PMID: 37110786 PMCID: PMC10141795 DOI: 10.3390/molecules28083553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Given their importance, hydrogen bonds (H-bonds) have been the subject of intense investigation since their discovery. Indeed, H-bonds play a fundamental role in determining the structure, the electronic properties, and the dynamics of complex systems, including biologically relevant materials such as DNA and proteins. While H-bonds have been largely investigated for systems in their electronic ground state, fewer studies have focused on how the presence of H-bonds could affect the static and dynamic properties of electronic excited states. This review presents an overview of the more relevant progress in studying the role of H-bond interactions in modulating excited-state features in multichromophoric biomimetic complex systems. The most promising spectroscopic techniques that can be used for investigating the H-bond effects in excited states and for characterizing the ultrafast processes associated with their dynamics are briefly summarized. Then, experimental insights into the modulation of the electronic properties resulting from the presence of H-bond interactions are provided, and the role of the H-bond in tuning the excited-state dynamics and the related photophysical processes is discussed.
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Affiliation(s)
- Elisa Fresch
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Elisabetta Collini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
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11
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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