1
|
Tang Z, Ma D, Yang J, Chen J, Lin Z, Liang Q, Jiao Y, Qu W, Xia D. Solar-driven strongly coupled plasmonic Au nanoarrays on mesoporous silica nanodisks enable selective fungal and bacterial inactivation in well water. WATER RESEARCH 2023; 245:120612. [PMID: 37729695 DOI: 10.1016/j.watres.2023.120612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/13/2023] [Accepted: 09/09/2023] [Indexed: 09/22/2023]
Abstract
Well water is an important water source in isolated rural areas but easily suffers from microbial contamination. Herein, we anchored periodic Au nanoarrays on mesoporous silica nanodisks (Au-MSN) to fabricate a solar-driven nano-stove for well water disinfection. The solar/Au-MSN process completely inactivated 3.98, 6.55, 7.11 log10 cfu/mL, and 3.37 log10 pfu/mL of Aspergillus niger spores, Escherichia coli, chlorine-resistant Spingopyxis sp. BM1-1, and bacteriophage MS2 within 5 min, respectively. Moreover, the complete inactivation of various microorganisms (even at a viable but nonculturable state) was achieved in the flow-through reactor under natural solar light in real well water matrixes. Thorough characterizations and theoretical simulations verified that the densely anchoring strategy of Au-MSN's nanoarray worked on broadband absorption via the photon confinement effect, and trace amounts of Au can induce strong electromagnetic fields and collective localized heating. The resulting surge of 1O2 and heat synergically destroyed membranes, dysfunction cellular self-defense and metabolic system, induced intracellular oxidative stress, and ultimately inactivated microorganisms. Additionally, the 1O2-dominated oxidation and cell adhesion facilitated the selective disinfection in real well water matrixes. This study provides a cost-effective and practical solution for efficient well water disinfection, which assists isolated rural areas in getting safe drinking water.
Collapse
Affiliation(s)
- Zhuoyun Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Dingren Ma
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Jingling Yang
- School of Environment, Jinan University, Guangzhou 510632, China
| | - Jinjuan Chen
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhuohang Lin
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Qiwen Liang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Yimu Jiao
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Wei Qu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Dehua Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou 510275, China.
| |
Collapse
|
2
|
Wang A, Yue K, Wei Y, Zhong W, Zhang G. Temperature‐induced structural change of integrin αvβ3 receptor and its interaction with the
RGD
peptide ligand. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anqi Wang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Kai Yue
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Yiang Wei
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
| | - Weishen Zhong
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| | - Genpei Zhang
- School of Energy and Environmental Engineering University of Science and Technology Beijing Beijing China
- Shunde Graduate School of University of Science and Technology Beijing Shunde Guangdong Province China
| |
Collapse
|
3
|
Gao Y, Wang B, Hu S, Zhu T, Zhang JZH. An efficient method to predict protein thermostability in alanine mutation. Phys Chem Chem Phys 2022; 24:29629-29639. [PMID: 36449314 DOI: 10.1039/d2cp04236c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The relationship between protein sequence and its thermodynamic stability is a critical aspect of computational protein design. In this work, we present a new theoretical method to calculate the free energy change (ΔΔG) resulting from a single-point amino acid mutation to alanine in a protein sequence. The method is derived based on physical interactions and is very efficient in estimating the free energy changes caused by a series of alanine mutations from just a single molecular dynamics (MD) trajectory. Numerical calculations are carried out on a total of 547 alanine mutations in 19 diverse proteins whose experimental results are available. The comparison between the experimental ΔΔGexp and the calculated values shows a generally good correlation with a correlation coefficient of 0.67. Both the advantages and limitations of this method are discussed. This method provides an efficient and valuable tool for protein design and engineering.
Collapse
Affiliation(s)
- Ya Gao
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Bo Wang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
| | - Shiyu Hu
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China. .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China. .,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Shenzhen Institute of Synthetic Biology, Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| |
Collapse
|
4
|
Maksum IP, Yosua Y, Nabiel A, Pratiwi RD, Sriwidodo S, Soedjanaatmadja UM. Refolding of bioactive human epidermal growth factor from E. coli BL21(DE3) inclusion bodies & evaluations on its in vitro & in vivo bioactivity. Heliyon 2022; 8:e09306. [PMID: 35497033 PMCID: PMC9039848 DOI: 10.1016/j.heliyon.2022.e09306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/10/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Human epidermal growth factor (hEGF) is a mitogenic protein widely used in pharmaceutical and cosmetic industries, thus recombinant DNA technology has been applied to meet the high demand for hEGF. The overexpression of recombinant protein in E. coli often leads to the formation of inclusion bodies (IBs). Mild solubilisation preserves the native secondary protein structure in IBs, thereby the high recovery of active protein from IBs. The redox system also plays a pivotal role in the formation of disulphide bonds during refolding of disulphide bond-containing protein. This study aimed to recover hEGF from bacterial IBs through freeze-thawing solubilisation and glutathione-based oxidative refolding. CBD-Ssp DnaB-hEGF fusion protein was expressed as IBs in E. coli, washed with Triton X-100 and urea to remove most protein contaminants, then the solubilised fusion protein was obtained by freeze-thawing with the addition of 2 M urea. The solubilised protein was subsequently refolded by intein cleavage via a glutathione-based redox system. The refolded hEGF demonstrated heat-resistant properties, interacted with specific antibodies on ELISA, stimulated keratinocyte proliferation and possessed significant in vivo wound healing properties on the 8th day, confirming that hEGF was correctly folded. In summary, the protocol described is suitable for the recovery of refolded hEGF from bacterial IBs by mild solubilisation and oxidative refolding.
Collapse
Affiliation(s)
- Iman Permana Maksum
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Yosua Yosua
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ahmad Nabiel
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Riyona Desvy Pratiwi
- Research Centre of Biotechnology, Indonesian Institute of Science, Bogor, Indonesia
| | - Sriwidodo Sriwidodo
- Department of Pharmaceutics & Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ukun M.S. Soedjanaatmadja
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| |
Collapse
|
5
|
Kang P, Xie C, Fall O, Randrianalisoa J, Qin Z. Computational Investigation of Protein Photoinactivation by Molecular Hyperthermia. J Biomech Eng 2021; 143:031004. [PMID: 33156335 PMCID: PMC7871998 DOI: 10.1115/1.4049017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 10/08/2020] [Indexed: 12/30/2022]
Abstract
To precisely control protein activity in a living system is a challenging yet long-pursued objective in biomedical sciences. Recently, we have developed a new approach named molecular hyperthermia (MH) to photoinactivate protein activity of interest without genetic modification. MH utilizes nanosecond laser pulse to create nanoscale heating around plasmonic nanoparticles to inactivate adjacent protein in live cells. Here we use a numerical model to study important parameters and conditions for MH to efficiently inactivate proteins in nanoscale. To quantify the protein inactivation process, the impact zone is defined as the range where proteins are inactivated by the nanoparticle localized heating. Factors that reduce the MH impact zone include the laser pulse duration, temperature-dependent thermal conductivity (versus constant properties), and nonspherical nanoparticle geometry. In contrast, the impact zone is insensitive to temperature-dependent material density and specific heat, as well as thermal interface resistance based on reported data in the literature. The low thermal conductivity of cytoplasm increases the impact zone. Different proteins with various Arrhenius kinetic parameters have significantly different impact zones. This study provides guidelines to design the protein inactivation process by MH.
Collapse
Affiliation(s)
- Peiyuan Kang
- Department of Mechanical Engineering, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080
| | - Chen Xie
- Department of Mechanical Engineering, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080
| | - Oumar Fall
- Department of Mechanical Engineering, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080;Ecole nationale Supérieure d'Ingénieur de Reims (ESIReims), University of Reims Champagne‐Ardenne, 3 Esplanade Roland Garros, Reims 51100, France
| | - Jaona Randrianalisoa
- Institut de Thermique, Mécanique, Matériaux (ITheMM), EA 7548, Université de Reims Champagne-Ardenne, Campus du Moulin de la Housse, F-51687, Reims, France
| | - Zhenpeng Qin
- Department of Mechanical Engineering, Department of Bioengineering, Center for Advanced Pain Studies, University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080;Department of Surgery, University of Texas at Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390
| |
Collapse
|
6
|
Peng C, Wang J, Shi Y, Xu Z, Zhu W. Increasing the Sampling Efficiency of Protein Conformational Change by Combining a Modified Replica Exchange Molecular Dynamics and Normal Mode Analysis. J Chem Theory Comput 2020; 17:13-28. [PMID: 33351613 DOI: 10.1021/acs.jctc.0c00592] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding conformational change at an atomic level is significant when determining a protein functional mechanism. Replica exchange molecular dynamics (REMD) is a widely used enhanced sampling method to explore protein conformational space. However, REMD with an explicit solvent model requires huge computational resources, immensely limiting its application. In this study, a variation of parallel tempering metadynamics (PTMetaD) with the omission of solvent-solvent interactions in exchange attempts and the use of low-frequency modes calculated by normal-mode analysis (NMA) as collective variables (CVs), namely ossPTMetaD, is proposed with the aim to accelerate MD simulations simultaneously in temperature and geometrical spaces. For testing the performance of ossPTMetaD, five protein systems with diverse biological functions and motion patterns were selected, including large-scale domain motion (AdK), flap movement (HIV-1 protease and BACE1), and DFG-motif flip in kinases (p38α and c-Abl). The simulation results showed that ossPTMetaD requires much fewer numbers of replicas than temperature REMD (T-REMD) with a reduction of ∼70% to achieve a similar exchange ratio. Although it does not obey the detailed balance condition, ossPTMetaD provides consistent results with T-REMD and experimental data. The high accessibility of the large conformational change of protein systems by ossPTMetaD, especially in simulating the very challenging DFG-motif flip of protein kinases, demonstrated its high efficiency and robustness in the characterization of the large-scale protein conformational change pathway and associated free energy profile.
Collapse
Affiliation(s)
- Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Yulong Shi
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.,Open Studio for Druggability Research of Marine Lead Compounds, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China
| |
Collapse
|
7
|
Sarkar D, Kang P, Nielsen SO, Qin Z. Non-Arrhenius Reaction-Diffusion Kinetics for Protein Inactivation over a Large Temperature Range. ACS NANO 2019; 13:8669-8679. [PMID: 31268674 PMCID: PMC7384293 DOI: 10.1021/acsnano.9b00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding protein folding and unfolding has been a long-standing fundamental question and has important applications in manipulating protein activity in biological systems. Experimental investigations of protein unfolding have been predominately conducted by small temperature perturbations (e.g., temperature jump), while molecular simulations are limited to small time scales (microseconds) and high temperatures to observe unfolding. Thus, it remains unclear how fast a protein unfolds irreversibly and loses function (i.e., inactivation) across a large temperature range. In this work, using nanosecond pulsed heating of individual plasmonic nanoparticles to create precise localized heating, we examine the protein inactivation kinetics at extremely high temperatures. Connecting this with protein inactivation measurements at low temperatures, we observe that the kinetics of protein unfolding is less sensitive to temperature change at the higher temperatures, which significantly departs from the Arrhenius behavior extrapolated from low temperatures. To account for this effect, we propose a reaction-diffusion model that modifies the temperature-dependence of protein inactivation by introducing a diffusion limit. Analysis of the reaction-diffusion model provides general guidelines in the behavior of protein inactivation (reaction-limited, transition, diffusion-limited) across a large temperature range from physiological temperature to extremely high temperatures. We further demonstrate that the reaction-diffusion model is particularly useful for designing optimal operating conditions for protein photoinactivation. The experimentally validated reaction-diffusion kinetics of protein unfolding is an important step toward understanding protein-inactivation kinetics over a large temperature range. It has important applications including molecular hyperthermia and calls for future studies to examine this model for other protein molecules.
Collapse
Affiliation(s)
- Daipayan Sarkar
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Peiyuan Kang
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Steven O. Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Zhenpeng Qin
- Department of Mechanical Engineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Bioengineering, The University of Texas at Dallas, Richardson, TX 75080, USA
- Department of Surgery, The University of Texas at Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
8
|
Growth factor delivery: Defining the next generation platforms for tissue engineering. J Control Release 2019; 306:40-58. [DOI: 10.1016/j.jconrel.2019.05.028] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/15/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022]
|
9
|
Kang P, Chen Z, Nielsen SO, Hoyt K, D'Arcy S, Gassensmith JJ, Qin Z. Molecular Hyperthermia: Spatiotemporal Protein Unfolding and Inactivation by Nanosecond Plasmonic Heating. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:10.1002/smll.201700841. [PMID: 28696524 PMCID: PMC5686774 DOI: 10.1002/smll.201700841] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/05/2017] [Indexed: 05/18/2023]
Abstract
Spatiotemporal control of protein structure and activity in biological systems has important and broad implications in biomedical sciences as evidenced by recent advances in optogenetic approaches. Here, this study demonstrates that nanosecond pulsed laser heating of gold nanoparticles (GNP) leads to an ultrahigh and ultrashort temperature increase, coined as "molecular hyperthermia", which causes selective unfolding and inactivation of proteins adjacent to the GNP. Protein inactivation is highly dependent on both laser pulse energy and GNP size, and has a well-defined impact zone in the nanometer scale. It is anticipated that the fine control over protein structure and function enabled by this discovery will be highly enabling within a number of arenas, from probing the biophysics of protein folding/unfolding to the nanoscopic manipulation of biological systems via an optical trigger, to developing novel therapeutics for disease treatment without genetic modification.
Collapse
Affiliation(s)
- Peiyuan Kang
- Department of Mechanical Engineering, The University of Texas at Dallas 800 West Campbell Rd., Richardson, TX, 75080, USA
| | - Zhuo Chen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
| | - Steven O Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
| | - Kenneth Hoyt
- Department of Bioengineering, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
- Department of Radiology, The University of Texas at Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
| | - Jeremiah J Gassensmith
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
| | - Zhenpeng Qin
- Department of Mechanical Engineering, The University of Texas at Dallas 800 West Campbell Rd., Richardson, TX, 75080, USA
- Department of Bioengineering, The University of Texas at Dallas, 800 West Campbell Rd., Richardson, TX, 75080, USA
- Department of Surgery, The University of Texas at Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| |
Collapse
|
10
|
Kuznetsov A, Kivi R, Järv J. Computational modeling of acrylodan-labeled cAMP dependent protein kinase catalytic subunit unfolding. Comput Biol Chem 2016; 61:197-201. [PMID: 26896699 DOI: 10.1016/j.compbiolchem.2016.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 12/11/2015] [Accepted: 01/20/2016] [Indexed: 10/22/2022]
Abstract
Structure of the cAMP-dependent protein kinase catalytic subunit, where the asparagine residue 326 was replaced with acrylodan-cystein conjugate to implement this fluorescence reporter group into the enzyme, was modeled by molecular dynamics (MD) method and the positioning of the dye molecule in protein structure was characterized at temperatures 300K, 500K and 700K. It was found that the acrylodan moiety, which fluorescence is very sensitive to solvating properties of its microenvironment, was located on the surface of the native protein at 300K that enabled its partial solvation with water. At high temperatures the protein structure significantly changed, as the secondary and tertiary structure elements were unfolded and these changes were sensitively reflected in positioning of the dye molecule. At 700K complete unfolding of the protein occurred and the reporter group was entirely expelled into water. However, at 500K an intermediate of the protein unfolding process was formed, where the fluorescence reporter group was directed towards the protein interior and buried in the core of the formed molten globule state. This different positioning of the reporter group was in agreement with the two different shifts of emission spectrum of the covalently bound acrylodan, observed in the unfolding process of the protein.
Collapse
Affiliation(s)
- Aleksei Kuznetsov
- Institute of Chemistry, University of Tartu, 14A Ravila Str., 50411 Tartu, Estonia
| | - Rait Kivi
- Institute of Chemistry, University of Tartu, 14A Ravila Str., 50411 Tartu, Estonia
| | - Jaak Järv
- Institute of Chemistry, University of Tartu, 14A Ravila Str., 50411 Tartu, Estonia.
| |
Collapse
|
11
|
Kim H, Kim S, Jung Y, Han J, Yun JH, Chang I, Lee W. Probing the Folding-Unfolding Transition of a Thermophilic Protein, MTH1880. PLoS One 2016; 11:e0145853. [PMID: 26766214 PMCID: PMC4713090 DOI: 10.1371/journal.pone.0145853] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
The folding mechanism of typical proteins has been studied widely, while our understanding of the origin of the high stability of thermophilic proteins is still elusive. Of particular interest is how an atypical thermophilic protein with a novel fold maintains its structure and stability under extreme conditions. Folding-unfolding transitions of MTH1880, a thermophilic protein from Methanobacterium thermoautotrophicum, induced by heat, urea, and GdnHCl, were investigated using spectroscopic techniques including circular dichorism, fluorescence, NMR combined with molecular dynamics (MD) simulations. Our results suggest that MTH1880 undergoes a two-state N to D transition and it is extremely stable against temperature and denaturants. The reversibility of refolding was confirmed by spectroscopic methods and size exclusion chromatography. We found that the hyper-stability of the thermophilic MTH1880 protein originates from an extensive network of both electrostatic and hydrophobic interactions coordinated by the central β-sheet. Spectroscopic measurements, in combination with computational simulations, have helped to clarify the thermodynamic and structural basis for hyper-stability of the novel thermophilic protein MTH1880.
Collapse
Affiliation(s)
- Heeyoun Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Sangyeol Kim
- Department of Physics, Pusan National University, Busan, 609–735, Korea
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Jeongmin Han
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| | - Iksoo Chang
- Center for Proteome Biophysics, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 711–873, Korea
- Department of Brain and Cognitive Sciences, DGIST, Daegu, 711–873, Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul, 120–740, Korea
| |
Collapse
|
12
|
Qin Z, Balasubramanian SK, Wolkers WF, Pearce JA, Bischof JC. Correlated parameter fit of arrhenius model for thermal denaturation of proteins and cells. Ann Biomed Eng 2014; 42:2392-404. [PMID: 25205396 DOI: 10.1007/s10439-014-1100-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/23/2014] [Indexed: 12/12/2022]
Abstract
Thermal denaturation of proteins is critical to cell injury, food science and other biomaterial processing. For example protein denaturation correlates strongly with cell death by heating, and is increasingly of interest in focal thermal therapies of cancer and other diseases at temperatures which often exceed 50 °C. The Arrhenius model is a simple yet widely used model for both protein denaturation and cell injury. To establish the utility of the Arrhenius model for protein denaturation at 50 °C and above its sensitivities to the kinetic parameters (activation energy E a and frequency factor A) were carefully examined. We propose a simplified correlated parameter fit to the Arrhenius model by treating E a, as an independent fitting parameter and allowing A to follow dependently. The utility of the correlated parameter fit is demonstrated on thermal denaturation of proteins and cells from the literature as a validation, and new experimental measurements in our lab using FTIR spectroscopy to demonstrate broad applicability of this method. Finally, we demonstrate that the end-temperature within which the denaturation is measured is important and changes the kinetics. Specifically, higher E a and A parameters were found at low end-temperature (50 °C) and reduce as end-temperatures increase to 70 °C. This trend is consistent with Arrhenius parameters for cell injury in the literature that are significantly higher for clonogenics (45-50 °C) vs. membrane dye assays (60-70 °C). Future opportunities to monitor cell injury by spectroscopic measurement of protein denaturation are discussed.
Collapse
Affiliation(s)
- Zhenpeng Qin
- Department of Mechanical Engineering, University of Minnesota, 111 Church St. SE, Minneapolis, MN, 55455, USA
| | | | | | | | | |
Collapse
|
13
|
Wiebe H, Weinberg N. Theoretical volume profiles as a tool for probing transition states: folding kinetics. J Chem Phys 2014; 140:124105. [PMID: 24697422 DOI: 10.1063/1.4868549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mechanism by which conformational changes, particularly folding and unfolding, occur in proteins and other biopolymers has been widely discussed in the literature. Molecular dynamics (MD) simulations of protein folding present a formidable challenge since these conformational changes occur on a time scale much longer than what can be afforded at the current level of computational technology. Transition state (TS) theory offers a more economic description of kinetic properties of a reaction system by relating them to the properties of the TS, or for flexible systems, the TS ensemble (TSE). The application of TS theory to protein folding is limited by ambiguity in the definition of the TSE for this process. We propose to identify the TSE for conformational changes in flexible systems by comparison of its experimentally determined volumetric property, known as the volume of activation, to the structure-specific volume profile of the process calculated using MD. We illustrate this approach by its successful application to unfolding of a model chain system.
Collapse
Affiliation(s)
- H Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - N Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
14
|
Chen H, Zhou CH, Yang J. A modified rat model of exercise-induced renal injury and the protective effects of losartan and yishen huanji decoction. Ren Fail 2013; 35:951-7. [PMID: 23815502 DOI: 10.3109/0886022x.2013.808536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We modified a rat model of exercise-induced renal injury by forcing 4-week-old male Sprague-Dawley (SD) rats (the MOD group) running on a treadmill for 8 weeks under conditions of high temperature, high humidity, bearing weight with some additional stimulations. Compared with the control (CON) group, the traditional running group (TRA), the losartan potassium intervention running group (LOS) and the traditional Chinese medicine "Yishen Huanji Decoction" intervention running group (CHI), the urinary, biochemistry indicators, the concentrations of angiotensin II (Ang II) were significantly higher in the MOD group than in the TRA group. After 3--4 weeks and 8-week training program, the 24-h urine protein and NAG levels in the LOS group and CHI group were lower than in the MOD group respectively. The BUN and SCr levels in the CHI group were lower than in the MOD group and higher than in the LOS group. AngII concentrations in the LOS group were higher than the MOD group. The modified rat renal injury model induced greater lesions than the traditional model. High temperatures, humidity and weight bearing were critical factors to induce Ang II activation, which can aggravate renal injury. Losartan potassium and the "Yishen Huanji Decoction" can protect against renal injury.
Collapse
Affiliation(s)
- Hong Chen
- Department of Nephrology, Navy General Hospital of People's Liberation Army, 6 Fucheng Road, Beijing, China.
| | | | | |
Collapse
|
15
|
Horsch M, Niethammer C, Vrabec J, Hasse H. Computational Molecular Engineering as an Emerging Technology in Process Engineering. ITIT 2013. [DOI: 10.1524/itit.2013.0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline of “Computational Molecular Engineering (CME)” which makes basic research in soft matter physics fruitful for industrial applications. Within the coming decade, major breakthroughs can be reached if a research focus is placed on processes at interfaces, combining aspects where an increase in the accessible length and time scales due to massively parallel high-performance computing will lead to particularly significant improvements.
Collapse
|
16
|
Replica exchange molecular dynamics simulation of chitosan for drug delivery system based on carbon nanotube. J Mol Graph Model 2013; 39:183-92. [DOI: 10.1016/j.jmgm.2012.11.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 10/29/2012] [Accepted: 11/03/2012] [Indexed: 11/21/2022]
|
17
|
Zhang Z, Wang L, Gao Y, Zhang J, Zhenirovskyy M, Alexov E. Predicting folding free energy changes upon single point mutations. ACTA ACUST UNITED AC 2012; 28:664-71. [PMID: 22238268 DOI: 10.1093/bioinformatics/bts005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MOTIVATION The folding free energy is an important characteristic of proteins stability and is directly related to protein's wild-type function. The changes of protein's stability due to naturally occurring mutations, missense mutations, are typically causing diseases. Single point mutations made in vitro are frequently used to assess the contribution of given amino acid to the stability of the protein. In both cases, it is desirable to predict the change of the folding free energy upon single point mutations in order to either provide insights of the molecular mechanism of the change or to design new experimental studies. RESULTS We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein. It is based on variation of the molecular mechanics Generalized Born (MMGB) method, scaled with optimized parameters (sMMGB) and utilizing specific model of unfolded state. The corresponding mutations are built in silico and the predictions are tested against large dataset of 1109 mutations with experimentally measured changes of the folding free energy. Benchmarking resulted in root mean square deviation = 1.78 kcal/mol and slope of the linear regression fit between the experimental data and the calculations was 1.04. The sMMGB is compared with other leading methods of predicting folding free energy changes upon single mutations and results discussed with respect to various parameters. AVAILABILITY All the pdb files we used in this article can be downloaded from http://compbio.clemson.edu/downloadDir/mentaldisorders/sMMGB_pdb.rar. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zhe Zhang
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
| | | | | | | | | | | |
Collapse
|
18
|
Qin Z, Bischof JC. Thermophysical and biological responses of gold nanoparticle laser heating. Chem Soc Rev 2012; 41:1191-217. [DOI: 10.1039/c1cs15184c] [Citation(s) in RCA: 433] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
19
|
Hyperthermia Using Inorganic Nanoparticles. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-12-415769-9.00013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
|
20
|
Rosas-Trigueros JL, Correa-Basurto J, Benítez-Cardoza CG, Zamorano-Carrillo A. Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures. Protein Sci 2011; 20:2035-46. [PMID: 21936009 DOI: 10.1002/pro.740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/05/2011] [Accepted: 09/08/2011] [Indexed: 01/05/2023]
Abstract
Bax is a member of the Bcl-2 protein family that participates in mitochondrion-mediated apoptosis. In the early stages of the apoptotic pathway, this protein migrates from the cytosol to the outer mitochondrial membrane, where it is inserted and usually oligomerizes, making cytochrome c-compatible pores. Although several cellular and structural studies have been reported, a description of the stability of Bax at the molecular level remains elusive. This article reports molecular dynamics simulations of monomeric Bax at 300, 400, and 500 K, focusing on the most relevant structural changes and relating them to biological experimental results. Bax gradually loses its α-helices when it is submitted to high temperatures, yet it maintains its globular conformation. The resistance of Bax to adopt an extended conformation could be due to several interactions that were found to be responsible for maintaining the structural stability of this protein. Among these interactions, we found salt bridges, hydrophobic interactions, and hydrogen bonds. Remarkably, salt bridges were the most relevant to prevent the elongation of the structure. In addition, the analysis of our results suggests which conformational movements are implicated in the activation/oligomerization of Bax. This atomistic description might have important implications for understanding the functionality and stability of Bax in vitro as well as within the cellular environment.
Collapse
Affiliation(s)
- Jorge Luis Rosas-Trigueros
- SEPI de la ESCOM del Instituto Politécnico Nacional, Juan de Dios Bátiz y Miguel Othón de Mendizábal s/n, México DF, México
| | | | | | | |
Collapse
|