1
|
Das N, Khan T, Halder B, Ghosh S, Sen P. Macromolecular crowding effects on protein dynamics. Int J Biol Macromol 2024:136248. [PMID: 39374718 DOI: 10.1016/j.ijbiomac.2024.136248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 09/30/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024]
Abstract
Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.
Collapse
Affiliation(s)
- Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, UP, India
| | - Shreya Ghosh
- 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
|
2
|
Miyagawa A, Komatsu H, Nagatomo S, Nakatani K. Thermodynamic Complexation Mechanism of Zinc Ion with 8-Hydroxyquinoline-5-Sulfonic Acid in Molecular Crowding Environment. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121181] [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]
|
3
|
Zhang H, Ye YT, Deng JL, Zhao P, Mao YF, Chen ZX. Rapid unfolding of pig pancreas α-amylase: Kinetics, activity and structure evolution. Food Chem 2022; 368:130795. [PMID: 34411861 DOI: 10.1016/j.foodchem.2021.130795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/16/2022]
Abstract
α-Amylase plays an important role in food processing and in-vivo digestion. Many biological functions of α-amylase are affected by unfolding. The pre-steady-state rapid unfolding kinetics of α-amylase remains unknown. In this study, the rapid unfolding kinetics of porcine pancreatic α-amylase (PPA) with guanidine hydrochloride (GdmHCl) were investigated by stopped-flow spectroscopy. Structural characterization of PPA by fluorescence spectroscopy, and molecular dynamics simulation showed that the unfolding process of PPA might start from the internal active center, where the β-sheet structure was destroyed, followed by the exposure of hydrophobic amino acid residues. Further research revealed that GdmHCl denaturized PPA not by complexing with PPA. The surrounding H-bond network of water was changed by GdmHCl. This research improves our understanding of the unfolding kinetics of the PPA on the microsecond scale. It also provides the evidence experimentally of the surrounding water contribution to protein denaturization.
Collapse
Affiliation(s)
- Hai Zhang
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yu-Tong Ye
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Jun-Ling Deng
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Pei Zhao
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yu-Fen Mao
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Zhong-Xiu Chen
- Molecular Food Science Laboratory, College of Food & Biology Engineering, Zhejiang Gongshang University, Hangzhou 310018, China.
| |
Collapse
|
4
|
Oeller M, Sormanni P, Vendruscolo M. An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement. Sci Rep 2021; 11:21932. [PMID: 34753962 PMCID: PMC8578320 DOI: 10.1038/s41598-021-01126-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/18/2021] [Indexed: 02/02/2023] Open
Abstract
The solubility of proteins correlates with a variety of their properties, including function, production yield, pharmacokinetics, and formulation at high concentrations. High solubility is therefore a key requirement for the development of protein-based reagents for applications in life sciences, biotechnology, diagnostics, and therapeutics. Accurate solubility measurements, however, remain challenging and resource intensive, which limits their throughput and hence their applicability at the early stages of development pipelines, when long-lists of candidates are typically available in minute amounts. Here, we present an automated method based on the titration of a crowding agent (polyethylene glycol, PEG) to quantitatively assess relative solubility of proteins using about 200 µg of purified material. Our results demonstrate that this method is accurate and economical in material requirement and costs of reagents, which makes it suitable for high-throughput screening. This approach is freely-shared and based on a low cost, open-source liquid-handling robot. We anticipate that this method will facilitate the assessment of the developability of proteins and make it substantially more accessible.
Collapse
Affiliation(s)
- Marc Oeller
- grid.5335.00000000121885934Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Pietro Sormanni
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.
| |
Collapse
|
5
|
Park J, Lee M, Lee B, Castaneda N, Tetard L, Kang EH. Crowding tunes the organization and mechanics of actin bundles formed by crosslinking proteins. FEBS Lett 2020; 595:26-40. [PMID: 33020904 DOI: 10.1002/1873-3468.13949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 01/05/2023]
Abstract
Fascin and α-actinin form higher-ordered actin bundles that mediate numerous cellular processes including cell morphogenesis and movement. While it is understood crosslinked bundle formation occurs in crowded cytoplasm, how crowding affects the bundling activities of the two crosslinking proteins is not known. Here, we demonstrate how solution crowding modulates the organization and mechanical properties of fascin- and α-actinin-induced bundles, utilizing total internal reflection fluorescence and atomic force microscopy imaging. Molecular dynamics simulations support the inference that crowding reduces binding interaction between actin filaments and fascin or the calponin homology 1 domain of α-actinin evidenced by interaction energy and hydrogen bonding analysis. Based on our findings, we suggest a mechanism of crosslinked actin bundle assembly and mechanics in crowded intracellular environments.
Collapse
Affiliation(s)
- Jinho Park
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA
| | - Myeongsang Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Briana Lee
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA
| | - Nicholas Castaneda
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Laurene Tetard
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Ellen Hyeran Kang
- NanoScience Technology Center, University of Central Florida, Orlando, FL, USA.,Department of Materials Science and Engineering, University of Central Florida, Orlando, FL, USA.,Department of Physics, University of Central Florida, Orlando, FL, USA
| |
Collapse
|
6
|
Does macromolecular crowding compatible with enzyme stem bromelain structure and stability? Int J Biol Macromol 2019; 131:527-535. [DOI: 10.1016/j.ijbiomac.2019.03.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 01/21/2023]
|
7
|
Kang B, Jo S, Baek J, Nakamura F, Hwang W, Lee H. Role of mechanical flow for actin network organization. Acta Biomater 2019; 90:217-224. [PMID: 30928733 DOI: 10.1016/j.actbio.2019.03.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022]
Abstract
The major cytoskeletal protein actin forms complex networks to provide structural support and perform vital functions in cells. In vitro studies have revealed that the structure of the higher-order actin network is determined primarily by the type of actin binding protein (ABP). By comparison, there are far fewer studies about the role of the mechanical environment for the organization of the actin network. In particular, the duration over which cells reorganize their shape in response to functional demands is relatively short compared to the in vitro protein polymerization time, suggesting that such changes can influence the actin network formation. We hypothesize that mechanical flows in the cytoplasm generated by exogenous and endogenous stimulation play a key role in the spatiotemporal regulation of the actin architecture. To mimic cytoplasmic streaming, we generated a circulating flow using surface acoustic wave in a microfluidic channel and investigated its effect on the formation of networks by actin and ABPs. We found that the mechanical flow affected the orientation and thickness of actin bundles, depending on the type and concentration of ABPs. Our computational model shows that the extent of alignment and thickness of actin bundle are determined by the balance between flow-induced drag forces and the tendency of ABPs to crosslink actin filaments at given angles. These results suggest that local intracellular flows can affect the assembly dynamics and morphology of the actin cytoskeleton. STATEMENT OF SIGNIFICANCE: Spatiotemporal regulation of actin cytoskeleton structure is essential in many cellular functions. It has been shown that mechanical cues including an applied force and geometric boundary can alter the structural characteristics of actin network. However, even though the cytoplasm accounts for a large portion of the cell volume, the effect of the cytoplasmic streaming flow produced during cell dynamics on actin network organization has not been reported. In this study, we demonstrated that the mechanical flow exerted during actin network organization play an important role in determining the orientation and dimension of actin bundle network. Our result will be beneficial in understanding the mechanism of the actin network reorganization occurred during physiological and pathological processes.
Collapse
Affiliation(s)
- Byungjun Kang
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seunghan Jo
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jonghyeok Baek
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Fumihiko Nakamura
- School of Pharmaceutical Science and Technology, Health Sciences Platform, Tianjin University, Tianjin 300072, China
| | - Wonmuk Hwang
- Departments of Biomedical Engineering, Materials Science & Engineering, and Physics & Astronomy, Texas A&M University, College Station, TX 77843, USA; School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Hyungsuk Lee
- School of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea.
| |
Collapse
|
8
|
Castaneda N, Lee M, Rivera-Jacquez HJ, Marracino RR, Merlino TR, Kang H. Actin Filament Mechanics and Structure in Crowded Environments. J Phys Chem B 2019; 123:2770-2779. [PMID: 30817154 DOI: 10.1021/acs.jpcb.8b12320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cellular environment is crowded with high concentrations of macromolecules that significantly reduce accessible volume for biomolecular interactions. Reductions in cellular volume can generate depletion forces that affect protein assembly and stability. The mechanical and structural properties of actin filaments play critical roles in various cellular functions, including structural support, cell movement, division, and intracellular transport. Although the effects of molecular crowding on actin polymerization have been shown, how crowded environments affect filament mechanics and structure is unknown. In this study, we investigate the effects of solution crowding on the modulations of actin filament bending stiffness and conformations both in vitro and in silico. Direct visualization of thermally fluctuating filaments in the presence of crowding agents is achieved by fluorescence microscopy imaging. Biophysical analysis indicates that molecular crowding enhances filament's effective bending stiffness and reduces average filament lengths. Utilizing the all-atom molecular dynamics simulations, we demonstrate that molecular crowding alters filament conformations and intersubunit contacts that are directly coupled to the mechanical properties of filaments. Taken together, our study suggests that the interplay between excluded volume effects and nonspecific interactions raised from molecular crowding may modulate actin filament mechanics and structure.
Collapse
Affiliation(s)
- Nicholas Castaneda
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States
| | - Myeongsang Lee
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States
| | - Hector J Rivera-Jacquez
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States
| | - Ryan R Marracino
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States
| | - Theresa R Merlino
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States
| | - Hyeran Kang
- NanoScience Technology Center , University of Central Florida , Orlando , Florida 32826 , United States
| |
Collapse
|
9
|
Davis WJ, Denton AR. Influence of solvent quality on conformations of crowded polymers. J Chem Phys 2018; 149:124901. [PMID: 30278673 DOI: 10.1063/1.5043434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded polymers, we model polymers as penetrable ellipsoids, whose shape fluctuations are governed by the statistics of self-avoiding walks, appropriate for a polymer in a good solvent. Within this coarse-grained model, we perform Monte Carlo simulations of mixtures of polymers and hard-nanosphere crowders, including trial changes in polymer size and shape. Penetration of polymers by crowders is incorporated via a free energy cost predicted by polymer field theory. To analyze the impact of crowding on polymer conformations in different solvents, we compute the average polymer shape distributions, radius of gyration, volume, and asphericity over ranges of the polymer-to-crowder size ratio and crowder volume fraction. The simulation results are accurately predicted by a free-volume theory of polymer crowding. Comparison of results for polymers in good and theta solvents indicates that excluded-volume interactions between polymer segments significantly affect crowding, especially in the limit of crowders much smaller than polymers. Our approach may help to motivate future experimental studies of polymers in crowded environments, with possible relevance for drug delivery and gene therapy.
Collapse
Affiliation(s)
- Wyatt J Davis
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| | - Alan R Denton
- Department of Physics, North Dakota State University, Fargo, North Dakota 58108-6050, USA
| |
Collapse
|