1
|
Higaki Y, Masuda T, Shiomoto S, Tanaka Y, Kiuchi H, Harada Y, Tanaka M. Pronounced Cold Crystallization and Hydrogen Bonding Distortion of Water Confined in Microphases of Double Zwitterionic Block Copolymer Aqueous Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:19612-19618. [PMID: 39227353 DOI: 10.1021/acs.langmuir.4c02254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Advanced materials leveraging water control are garnering considerable interest, with the state of water emerging as a critical aspect of material design. This study explored the impact of microphase separation on water using aqueous solutions of double zwitterionic diblock copolymers, specifically poly(carboxybetaine methacrylate) and poly(sulfobetaine methacrylate) (PCB2-b-PSB4). These copolymers form a mesoscale periodic ordered lattice structure consisting of two distinct aqueous phases. Through differential scanning calorimetry and X-ray emission spectroscopy, it was found that water in these PCB2-b-PSB4 aqueous solutions exhibits pronounced cold crystallization and subtle distortions in hydrogen-bonding configurations.
Collapse
Affiliation(s)
- Yuji Higaki
- Faculty of Science and Technology, Oita University, 700 Dannoharu, Oita 870-1192, Japan
| | - Takumi Masuda
- Graduate School of Engineering, Oita University, 700 Dannoharu, Oita 870-1192, Japan
| | - Shohei Shiomoto
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Yukiko Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hisao Kiuchi
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Synchrotron Radiation Research Organization, The University of Tokyo, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshihisa Harada
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Synchrotron Radiation Research Organization, The University of Tokyo, Sayo-gun, Hyogo 679-5148, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| |
Collapse
|
2
|
Demosthene B, Kravchuk P, Harmon CL, Kalae A, Kang EH. Small organic osmolytes accelerate actin filament assembly and stiffen filaments. Cytoskeleton (Hoboken) 2024. [PMID: 39276026 DOI: 10.1002/cm.21927] [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: 03/20/2024] [Revised: 08/27/2024] [Accepted: 09/03/2024] [Indexed: 09/16/2024]
Abstract
Actin filament assembly and mechanics are crucial for maintenance of cell structure, motility, and division. Actin filament assembly occurs in a crowded intracellular environment consisting of various types of molecules, including small organic molecules known as osmolytes. Ample evidence highlights the protective functions of osmolytes such as trimethylamine-N-oxide (TMAO), including their effects on protein stability and their ability to counteract cellular osmotic stress. Yet, how TMAO affects individual actin filament assembly dynamics and mechanics is not well understood. We hypothesize that, owing to its protective nature, TMAO will enhance filament dynamics and stiffen actin filaments due to increased stability. In this study, we investigate osmolyte-dependent actin filament assembly and bending mechanics by measuring filament elongation rates, steady-state filament lengths, and bending persistence lengths in the presence of TMAO using total internal reflection fluorescence microscopy and pyrene assays. Our results demonstrate that TMAO increases filament elongation rates as well as steady-state average filament lengths, and enhances filament bending stiffness. Together, these results will help us understand how small organic osmolytes modulate cytoskeletal protein assembly and mechanics in living cells.
Collapse
Affiliation(s)
- Bryan Demosthene
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA
| | - Pavlo Kravchuk
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Connor L Harmon
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Abdulrazak Kalae
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
| | - Ellen H Kang
- NanoScience Technology Center, University of Central Florida, Orlando, Florida, USA
- Department of Physics, University of Central Florida, Orlando, Florida, USA
- Department of Materials Science and Engineering, University of Central Florida, Orlando, Florida, USA
| |
Collapse
|
3
|
Silva HO, Rohwedder JJR, Nome RA. Femtosecond Terahertz Pulse Propagation Measurements and Simulations of Dewetting Kinetics in Real Time. ACS OMEGA 2024; 9:38107-38115. [PMID: 39281959 PMCID: PMC11391565 DOI: 10.1021/acsomega.4c05275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/30/2024] [Accepted: 08/20/2024] [Indexed: 09/18/2024]
Abstract
We report a terahertz time-domain study of dewetting kinetics on two time scales: femtoseconds and in real time (on the order of minutes). We recorded full electric field terahertz time domain signals with femtosecond time resolution during dewetting of water in cellulose. The femtosecond time-domain signals were analyzed with respect to the amplitude and signal emission times and how these two quantities changed over the course of dewetting kinetics. The femtosecond time-domain signals were modeled by a combination of finite-difference time-domain electromagnetic simulations of linear terahertz pulse propagation and an effective medium description of the dielectric permittivity. A logistic regression mechanism was incorporated into the electrodynamics simulations to account for the observed kinetics. In addition, analysis of the area-normalized, real-time time-dependent terahertz spectra was used to identify broad regions in the terahertz spectral range that correlated with the kinetic process. Real-time two-dimensional terahertz correlation maps were used to identify the pure rotational spectrum of water vapor, thus characterizing the evaporation part of the dewetting kinetics problem. We conclude with a kinetic model that accounts for our observations through a microscopic mechanism involving the interconversion among bulk water, water clusters, and individual water molecules in the gas phase. Overall, the approach presented here illustrates an application of femtosecond time-resolved experiments in the terahertz spectral range to the study of kinetic processes.
Collapse
Affiliation(s)
- Helen Oliveira Silva
- Institute of Chemistry, State University of Campinas, 13083-970 Campinas, Brazil
| | | | - René Alfonso Nome
- Institute of Chemistry, State University of Campinas, 13083-970 Campinas, Brazil
| |
Collapse
|
4
|
Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
Collapse
Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | |
Collapse
|
5
|
Penkov NV. Peculiarities of the Dynamical Hydration Shell of Native Conformation Protein Using a Bovine Serum Albumin Example. APPLIED SPECTROSCOPY 2024:37028241261097. [PMID: 38881287 DOI: 10.1177/00037028241261097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
This paper describes an approach based on the method of terahertz time-domain spectroscopy, which allows the analysis of dynamical hydration shells of proteins with a thickness of 1-2 nm. Using the example of bovine serum albumin in three conformations, it is shown that the hydration shells of the protein are characterized by increased binding of water molecules in the primary hydration layers, and in more distant areas of hydration, on the contrary, the water structure is somewhat destroyed. The fraction of free or weakly bound molecules, usually observed in the structure of liquid water in hydration shells, become more numerous but its average binding is greater than in undisturbed water. The energy distribution of hydrogen bonds in hydration shells is narrowed compared to undisturbed water. All these manifestations of hydration are most pronounced for the native conformation of the protein. Also, the hydration shells of the native protein are characterized by a smaller number of hydrogen bonds and a tendency to decrease their average energy compared to non-native conformations. The fact of a pronounced peculiarity of the hydration shells of the protein in the native conformation has been noted for different proteins before. However, the methodological approach used in this work for the first time allowed this peculiarity to be described by specific parameters of the intermolecular structure and dynamics of water.
Collapse
Affiliation(s)
- Nikita V Penkov
- Institute of Cell Biophysics, Federal Research Center, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Russia
| |
Collapse
|
6
|
Huang X, Li J, Araki Y, Wada T, Xu Y, Takai M. Enzyme stability in polymer hydrogel-enzyme hybrid nanocarrier containing phosphorylcholine group. RSC Adv 2024; 14:18807-18814. [PMID: 38863819 PMCID: PMC11166189 DOI: 10.1039/d4ra02436b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024] Open
Abstract
Enzymes are biological catalysts with good biocompatibility and high efficiency and have been widely used in many fields, such as wastewater treatment, biosensors, and the medical industry. However, their inherently low stability under conditions of practical use limits further applications. Zwitterionic polymers possessing a pair of oppositely charged groups in their repeating units can increase protein stability because of their good biocompatibility and high water content. In this study, zwitterionic copolymer nanogels comprising poly(2-methacryloyloxyethyl phosphorylcholine (MPC)-co-methacrylic acid-N-hydroxy succinimide ester (MNHS)) (PMS) were synthesized via reversible addition-fragmentation chain-transfer polymerization (RAFT). β-Galactosidase (β-gal) was post-modified within zwitterionic polymer nanogels with a covalently-bound spacer and the activity was compared with that of directly immobilized β-gal and free β-gal. Compared with direct immobilization, covalent immobilization with a spacer could reduce the structural change of β-gal, as confirmed by the circular dichroism spectra. Although the activity of β-gal decreased after immobilization, the hybrids of the β-gal immobilized nanogels, termed hybrid nanogel-enzymes, demonstrated superior stability compared to the free enzymes. The hybrid nanogel-enzymes maintained their function against inactivation by organic solvents and proteinases owing to their high water content, anti-biofouling properties, and limited mass transfer. They can also withstand protein aggregation at high temperatures and maintain their activity. Compared to direct immobilization, immobilization with a spacer resulted in a dramatic increase in the enzyme activity and a slight decrease in the stability. These results indicate that polymer nanogels containing phosphorylcholine units are promising materials for enzyme immobilization, expanding the scope of enzyme applications.
Collapse
Affiliation(s)
- Xuejin Huang
- Department of Bioengineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656 Tokyo Japan
| | - Jincai Li
- Department of Bioengineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656 Tokyo Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Sendai Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University Sendai Japan
| | - Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Metropolitan University Sakai Osaka Japan
| | - Madoka Takai
- Department of Bioengineering, School of Engineering, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku 113-8656 Tokyo Japan
| |
Collapse
|
7
|
Higuchi Y, Saleh MA, Anada T, Tanaka M, Hishida M. Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations. J Phys Chem B 2024; 128:5008-5017. [PMID: 38728154 DOI: 10.1021/acs.jpcb.3c08470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.
Collapse
Affiliation(s)
- Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Md Abu Saleh
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Takahisa Anada
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| |
Collapse
|
8
|
Trevitt CR, Yashwanth Kumar DR, Fowler NJ, Williamson MP. Interactions between the protein barnase and co-solutes studied by NMR. Commun Chem 2024; 7:44. [PMID: 38418894 PMCID: PMC10902301 DOI: 10.1038/s42004-024-01127-0] [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: 11/05/2023] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Protein solubility and stability depend on the co-solutes present. There is little theoretical basis for selection of suitable co-solutes. Some guidance is provided by the Hofmeister series, an empirical ordering of anions according to their effect on solubility and stability; and by osmolytes, which are small organic molecules produced by cells to allow them to function in stressful environments. Here, NMR titrations of the protein barnase with Hofmeister anions and osmolytes are used to measure and locate binding, and thus to separate binding and bulk solvent effects. We describe a rationalisation of Hofmeister (and inverse Hofmeister) effects, which is similar to the traditional chaotrope/kosmotrope idea but based on solvent fluctuation rather than water withdrawal, and characterise how co-solutes affect protein stability and solubility, based on solvent fluctuations. This provides a coherent explanation for solute effects, and points towards a more rational basis for choice of excipients.
Collapse
Affiliation(s)
- Clare R Trevitt
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
- Certara UK Ltd, Level 2-Acero, 1 Concourse Way, Sheffield, S1 3BJ, UK
| | | | - Nicholas J Fowler
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
| |
Collapse
|
9
|
Hishida M. Correlation between Hydration States and Self-assembly Structures of Phospholipid and Surfactant Studied by Terahertz Spectroscopy. J Oleo Sci 2024; 73:419-427. [PMID: 38556277 DOI: 10.5650/jos.ess23188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024] Open
Abstract
Phospholipids and surfactants form membranes and other self-assembled structures in water. However, it is not fully understood how the surrounding water (hydration water) is involved in their structure formation. In this paper, I summarize the results of our investigation of the long-range hydration state of phospholipids and surfactants at their surfaces by means of terahertz spectroscopy. By observing the collective rotational dynamics of water in the picosecond time scale, this technique allows us to observe not only the water directly bound to the solute, but also the weakly affected water outside of it. For example, PC phospholipids inhibit water dynamics over long distances, whereas PE phospholipids make water more mobile than bulk water. The causes of this difference in hydration and how it is involved in the structural formation of the membrane are reviewed.
Collapse
Affiliation(s)
- Mafumi Hishida
- Department of Chemistry, Faculty of Science, Tokyo University of Science
| |
Collapse
|
10
|
Khan T, Das N, Negi KS, Bhowmik S, Sen P. Understanding the intricacy of protein in hydrated deep eutectic solvent: Solvation dynamics, conformational fluctuation dynamics, and stability. Int J Biol Macromol 2023; 253:127100. [PMID: 37778586 DOI: 10.1016/j.ijbiomac.2023.127100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Deep eutectic solvents (DESs) are potential biocatalytic media due to their easy preparation, fine-tuneability, biocompatibility, and most importantly, due to their ability to keep protein stable and active. However, there are many unanswered questions and gaps in our knowledge about how proteins behave in these alternate media. Herein, we investigated solvation dynamics, conformational fluctuation dynamics, and stability of human serum albumin (HSA) in 0.5 Acetamide/0.3 Urea/0.2 Sorbitol (0.5Ac/0.3Ur/0.2Sor) DES of varying concentrations to understand the intricacy of protein behaviour in DES. Our result revealed a gradual decrease in the side-chain flexibility and thermal stability of HSA beyond 30 % DES. On the other hand, the associated water dynamics around domain-I of HSA decelerate only marginally with increasing DES content, although viscosity rises considerably. We propose that even though macroscopic solvent properties are altered, a protein feels only an aqueous type of environment in the presence of DES. This is probably the first experimental study to delineate the role of the associated water structure of the enzyme for maintaining its stability inside DES. Although considerable effort is necessary to generalize such claims, it might serve as the basis for understanding why proteins remain stable and active in DES.
Collapse
Affiliation(s)
- Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Suman Bhowmik
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India.
| |
Collapse
|
11
|
Peters J, Oliva R, Caliò A, Oger P, Winter R. Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions. Chem Rev 2023; 123:13441-13488. [PMID: 37943516 DOI: 10.1021/acs.chemrev.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.
Collapse
Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 140 rue de la physique, 38400 St Martin d'Hères, France
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble, France
- Institut Universitaire de France, 75005 Paris, France
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy
| | - Antonino Caliò
- European Synchrotron Radiation Facility, 71 avenue des Martyrs, 38000 Grenoble, France
| | - Philippe Oger
- INSA Lyon, Universite Claude Bernard Lyon1, CNRS, UMR5240, 69621 Villeurbanne, France
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Dortmund, Otto-Hahn-Str. 4a, D-44227 Dortmund, Germany
| |
Collapse
|
12
|
Negi KS, Das N, Khan T, Sen P. Osmolyte induced protein stabilization: modulation of associated water dynamics might be a key factor. Phys Chem Chem Phys 2023; 25:32602-32612. [PMID: 38009208 DOI: 10.1039/d3cp03357k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
The mechanism of protein stabilization by osmolytes remains one of the most important and long-standing puzzles. The traditional explanation of osmolyte-induced stability through the preferential exclusion of osmolytes from the protein surface has been seriously challenged by the observations like the concentration-dependent reversal of osmolyte-induced stabilization/destabilization. The more modern explanation of protein stabilization/destabilization by osmolytes considers an indirect effect due to osmolyte-induced distortion of the water structure. It provides a general mechanism, but there are numerous examples of protein-specific effects, i.e., a particular osmolyte might stabilize one protein, but destabilize the other, that could not be rationalized through such an explanation. Herein, we hypothesized that osmolyte-induced modulation of associated water might be a critical factor in controlling protein stability in such a medium. Taking different osmolytes and papain as a protein, we proved that our proposal could explain protein stability in osmolyte media. Stabilizing osmolytes rigidify associated water structures around the protein, whereas destabilizing osmolytes make them flexible. The strong correlation between the stability and the associated water dynamics, and the fact that such dynamics are very much protein specific, established the importance of considering the modulation of associated water structures in explaining the osmolyte-induced stabilization/destabilization of proteins. More interestingly, we took another protein, bromelain, for which a traditionally stabilizing osmolyte, sucrose, acts as a stabilizer at higher concentrations but as a destabilizer at lower concentrations. Our proposal successfully explains such observations, which is probably impossible by any known mechanisms. We believe this report will trigger much research in this area.
Collapse
Affiliation(s)
- Kuldeep Singh Negi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur-208016, Uttar Pradesh, India.
| |
Collapse
|
13
|
Penkov NV. Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules. Biophys Rev 2023; 15:833-849. [PMID: 37974994 PMCID: PMC10643733 DOI: 10.1007/s12551-023-01131-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/30/2023] [Indexed: 11/19/2023] Open
Abstract
The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.
Collapse
Affiliation(s)
- Nikita V. Penkov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics RAS, 142290 Pushchino, Russia
| |
Collapse
|
14
|
Hishida M, Kaneko A, Yamamura Y, Saito K. Contrasting Changes in Strongly and Weakly Bound Hydration Water of a Protein upon Denaturation. J Phys Chem B 2023; 127:6296-6305. [PMID: 37417885 PMCID: PMC10364084 DOI: 10.1021/acs.jpcb.3c02970] [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: 05/05/2023] [Revised: 06/21/2023] [Indexed: 07/08/2023]
Abstract
Water is considered integral for the stabilization and function of proteins, which has recently attracted significant attention. However, the microscopic aspects of water ranging up to the second hydration shell, including strongly and weakly bound water at the sub-nanometer scale, are not yet well understood. Here, we combined terahertz spectroscopy, thermal measurements, and infrared spectroscopy to clarify how the strongly and weakly bound hydration water changes upon protein denaturation. With denaturation, that is, the exposure of hydrophobic groups in water and entanglement of hydrophilic groups, the number of strongly bound hydration water decreased, while the number of weakly bound hydration water increased. Even though the constraint of water due to hydrophobic hydration is weak, it extends to the second hydration shell as it is caused by the strengthening of hydrogen bonds between water molecules, which is likely the key microscopic mechanism for the destabilization of the native state due to hydration.
Collapse
Affiliation(s)
- Mafumi Hishida
- Department
of Chemistry, Faculty of Science, Tokyo
University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 162-8601, Japan
| | - Ayumi Kaneko
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yasuhisa Yamamura
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Kazuya Saito
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| |
Collapse
|
15
|
Sugiyama JI, Tokunaga Y, Hishida M, Tanaka M, Takeuchi K, Satoh D, Imashimizu M. Nonthermal acceleration of protein hydration by sub-terahertz irradiation. Nat Commun 2023; 14:2825. [PMID: 37217486 DOI: 10.1038/s41467-023-38462-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
The collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxation (DR) measurements to investigate how externally applied sub-THz electromagnetic fields perturb the rapid collective dynamics and influence the considerably slower chemical processes in protein-water systems. We analyzed an aqueous lysozyme solution, whose hydration is not thermally equilibrated. By detecting time-lapse differences in microwave DR, we demonstrated that sub-THz irradiation gradually decreases the dielectric permittivity of the lysozyme solution by reducing the orientational polarization of water molecules. Comprehensive analysis combining THz and nuclear magnetic resonance spectroscopies suggested that the gradual decrease in the dielectric permittivity is not induced by heating but is due to a slow shift toward the hydrophobic hydration structure in lysozyme. Our findings can be used to investigate hydration-mediated protein functions based on sub-THz irradiation.
Collapse
Affiliation(s)
- Jun-Ichi Sugiyama
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565, Japan
| | - Yuji Tokunaga
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Mafumi Hishida
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8571, Japan
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Masahito Tanaka
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Daisuke Satoh
- Research Institute for Measurement and Analytical Instrumentation, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8568, Japan
| | - Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8565, Japan.
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Irukuvajjula SS, Jithender Reddy G, Rao K, Vadrevu LR. Contrasting effect of ficoll on apo and holo forms of bacterial chemotaxis protein Y: Selective destabilization of the conformationally altered holo form. Int J Biol Macromol 2023; 232:123505. [PMID: 36736516 DOI: 10.1016/j.ijbiomac.2023.123505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023]
Abstract
Chemotaxis Y (CheY), upon metal binding, displays a drastic alteration in its structure and stability. This premise prompted us to study the effect of crowding on the two conformationally distinct states of the same test protein. A comparative analysis on the structure and thermal stability in the presence and absence of the macromolecular crowder, ficoll, and its monomeric unit, sucrose, revealed a contrasting effect of ficoll on the apo and holo forms. In the presence of ficoll while the thermal stability (Tm) of the apo form is enhanced, the thermal stability of the holo form is reduced. The selective lowering of Tm for the holo form in the combined presence of ficoll and sucrose and not in sucrose alone suggests that the contrasting effect is due to the macromolecular nature of ficoll. Since metal-protein interaction remains unperturbed in the presence of ficoll and Mg2+ sequestration is ruled out in a systematic manner the alternative possibility for the exclusive reduction in the thermal stability of the holo form is the ficoll-induced modulation of the relative population of apo and holo forms of CheY.
Collapse
Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India.
| | - G Jithender Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Krishna Rao
- Tata Institute of Fundamental Research, 36/P, Gopanpally Mandal, Ranga Reddy District, Hyderabad, Telangana State 500107, India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Science and Technology - Pilani, Hyderabad Campus, Shamirpet, Hyderabad 500078, India
| |
Collapse
|
18
|
Hu K, Shirakashi R. Molecular dynamics study of water rotational relaxation in saccharide solution for the development of bioprotective agent. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
19
|
Meena P, Kishore N. Synergistic effects of osmolytes on solvent exclusion and resulting protein stabilization: Studies with sucrose, taurine and sorbitol individually and in combination. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
20
|
Somero GN. Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:389-413. [PMID: 37073170 PMCID: PMC10077225 DOI: 10.1007/s42995-022-00140-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/15/2022] [Indexed: 05/03/2023]
Abstract
The seas confront organisms with a suite of abiotic stressors that pose challenges for physiological activity. Variations in temperature, hydrostatic pressure, and salinity have potential to disrupt structures, and functions of all molecular systems on which life depends. During evolution, sequences of nucleic acids and proteins are adaptively modified to "fit" these macromolecules for function under the particular abiotic conditions of the habitat. Complementing these macromolecular adaptations are alterations in compositions of solutions that bathe macromolecules and affect stabilities of their higher order structures. A primary result of these "micromolecular" adaptations is preservation of optimal balances between conformational rigidity and flexibility of macromolecules. Micromolecular adaptations involve several families of organic osmolytes, with varying effects on macromolecular stability. A given type of osmolyte generally has similar effects on DNA, RNA, proteins and membranes; thus, adaptive regulation of cellular osmolyte pools has a global effect on macromolecules. These effects are mediated largely through influences of osmolytes and macromolecules on water structure and activity. Acclimatory micromolecular responses are often critical in enabling organisms to cope with environmental changes during their lifetimes, for example, during vertical migration in the water column. A species' breadth of environmental tolerance may depend on how effectively it can vary the osmolyte composition of its cellular fluids in the face of stress. Micromolecular adaptations remain an under-appreciated aspect of evolution and acclimatization. Further study can lead to a better understanding of determinants of environmental tolerance ranges and to biotechnological advances in designing improved stabilizers for biological materials.
Collapse
Affiliation(s)
- George N. Somero
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950 USA
| |
Collapse
|
21
|
Kamali A, Jahmidi-Azizi N, Oliva R, Winter R. Deep sea osmolytes in action: their effect on protein-ligand binding under high pressure stress. Phys Chem Chem Phys 2022; 24:17966-17978. [PMID: 35775876 DOI: 10.1039/d2cp01769e] [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
Because organisms living in the deep sea and in the sub-seafloor must be able to cope with hydrostatic pressures up to 1000 bar and more, their biomolecular processes, including ligand-binding reactions, must be adjusted to keep the associated volume changes low in order to function efficiently. Almost all organisms use organic cosolvents (osmolytes) to protect their cells from adverse environmental conditions. They counteract osmotic imbalance, stabilize the structure of proteins and maintain their function. We studied the binding properties of the prototypical ligand proflavine to two serum proteins with different binding pockets, BSA and HSA, in the presence of two prominent osmolytes, trimethylamine-N-oxide (TMAO) and glycine betaine (GB). TMAO and GB play an important role in the regulation and adaptation of life in deep-sea organisms. To this end, pressure dependent fluorescence spectroscopy was applied, supplemented by circular dichroism (CD) spectroscopy and computer modeling studies. The pressure-dependent measurements were also performed to investigate the intimate nature of the complex formation in relation to hydration and packing changes caused by the presence of the osmolytes. We show that TMAO and GB are able to modulate the ligand binding process in specific ways. Depending on the chemical make-up of the protein's binding pocket and thus the thermodynamic forces driving the binding process, there are osmolytes with specific interaction sites and binding strengths with water that are able to mediate efficient ligand binding even under external stress conditions. In the binding of proflavine to BSA and HSA, the addition of both compatible osmolytes leads to an increase in the binding constant upon pressurization, with TMAO being the most efficient, rendering the binding process also insensitive to pressurization even up to 2 kbar as the volume change remains close to zero. This effect can be corroborated by the effects the cosolvents impose on the strength and dynamics of hydration water as well as on the conformational dynamics of the protein.
Collapse
Affiliation(s)
- Armin Kamali
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| | - Nisrine Jahmidi-Azizi
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| | - Rosario Oliva
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy.
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Street 4a, 44227 Dortmund, Germany.
| |
Collapse
|
22
|
Nishida K, Anada T, Tanaka M. Roles of interfacial water states on advanced biomedical material design. Adv Drug Deliv Rev 2022; 186:114310. [PMID: 35487283 DOI: 10.1016/j.addr.2022.114310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 12/15/2022]
Abstract
When biomedical materials come into contact with body fluids, the first reaction that occurs on the material surface is hydration; proteins are then adsorbed and denatured on the hydrated material surface. The amount and degree of denaturation of adsorbed proteins affect subsequent cell behavior, including cell adhesion, migration, proliferation, and differentiation. Biomolecules are important for understanding the interactions and biological reactions of biomedical materials to elucidate the role of hydration in biomedical materials and their interaction partners. Analysis of the water states of hydrated materials is complicated and remains controversial; however, knowledge about interfacial water is useful for the design and development of advanced biomaterials. Herein, we summarize recent findings on the hydration of synthetic polymers, supramolecular materials, inorganic materials, proteins, and lipid membranes. Furthermore, we present recent advances in our understanding of the classification of interfacial water and advanced polymer biomaterials, based on the intermediate water concept.
Collapse
Affiliation(s)
- Kei Nishida
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan; Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Japan(1)
| | - Takahisa Anada
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering Kyushu university, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan.
| |
Collapse
|