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Shuvo MN, Halder SK, Alam N, Himel MK, Shil A. Developing phytocompound-based new drugs against multi-drug-resistant Staphylococcus aureus. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231475. [PMID: 39050719 PMCID: PMC11265916 DOI: 10.1098/rsos.231475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 05/28/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024]
Abstract
Staphylococcus aureus, a prevalent component of the human microbiota, is associated with skin infections to life-threatening diseases, presenting challenges in treatment options and necessitating the development of effective treatments. This study integrated computational and in vitro approaches to identify promising phytocompounds with therapeutic potential. Staphopain B emerged as a target protein for its role in immune evasion, exhibiting stability during molecular dynamic simulation (MDS) with a root mean square deviation value of 2.376 Å. Screening 115 phytocompounds with antibacterial properties from the PubChem database identified 12 with drug-like properties, nine of which showed superior binding affinity to Staphopain B compared to a commercial antibiotic, doxycycline (-7.8 kcal mol-1). Notably, epoxyazadiradione and nimbolide displayed higher estimated free energy of binding scores (-7.91 and -7.93 kcal mol-1, respectively), indicating strong protein-ligand interactions. The root mean square fluctuation values for epoxyazadiradione and nimbolide were 1.097 and 1.034 Å, respectively, which was confirmed through MDS. Crude ethanolic extracts (100% and 70%) of neem (Azadirachta indica) leaves demonstrated narrow inhibition against the bacteria in comparison to doxycycline in the disc-diffusion assay. This study underscores the potential of phytocompounds as therapeutic agents against S. aureus; however, further in vitro experiments and testing of the phytocompounds in vivo are required.
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Affiliation(s)
| | | | - Nuhu Alam
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
| | - Mahbubul Kabir Himel
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
| | - Aparna Shil
- Department of Botany, Jahangirnagar University, Savar, Dhaka1342, Bangladesh
- Padma Bioresearch, Dhaka1342, Bangladesh
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2
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Du Z, Huang X, Li H, Zheng M, Hong T, Li Z, Du X, Jiang Z, Ni H, Li Q, Zhu Y. Improvement of thermostability by increasing rigidity in the finger regions and flexibility in the catalytic pocket area of Pseudoalteromonas porphyrae κ-carrageenase. World J Microbiol Biotechnol 2024; 40:216. [PMID: 38802708 DOI: 10.1007/s11274-024-04029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Poor thermostability reduces the industrial application value of κ-carrageenase. In this study, the PoPMuSiC algorithm combined with site-directed mutagenesis was applied to improve the thermostability of the alkaline κ-carrageenase from Pseudoalteromonas porphyrae. The mutant E154A with improved thermal stability was successfully obtained using this strategy after screening seven rationally designed mutants. Compared with the wild-type κ-carrageenase (WT), E154A improved the activity by 29.4% and the residual activity by 51.6% after treatment at 50 °C for 30 min. The melting temperature (Tm) values determined by circular dichroism were 66.4 °C and 64.6 °C for E154A and WT, respectively. Molecular dynamics simulation analysis of κ-carrageenase showed that the flexibility decreased within the finger regions (including F1, F2, F3, F5 and F6) and the flexibility improved in the catalytic pocket area of the mutant E154A. The catalytic tunnel dynamic simulation analysis revealed that E154A led to enlarged catalytic tunnel volume and increased rigidity of the enzyme-substrate complex. The increasing rigidity within the finger regions and more flexible catalytic pocket of P. porphyrae κ-carrageenase might be a significant factor for improvement of the thermostability of the mutant κ-carrageenase E154A. The proposed rational design strategy could be applied to improve the enzyme kinetic stability of other industrial enzymes. Moreover, the hydrolysates of κ-carrageenan digested by the mutant E154A demonstrated increased scavenging activities against hydroxyl (OH) radicals and 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radicals compared with the undigested κ-carrageenan.
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Affiliation(s)
- Zeping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Xiaoyi Huang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Tao Hong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Xiping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
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3
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Benrezkallah D. Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. J Mol Graph Model 2024; 127:108700. [PMID: 38183846 DOI: 10.1016/j.jmgm.2023.108700] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Most life forms on earth live at temperatures below 50 °C. Within these organisms are proteins that form the three-dimensional structures essential to their biological activity and function. However, some thermophilic life forms can resist higher temperatures and have corresponding adaptations to preserve protein function at these high temperatures. Among the structural factors responsible for this resistance of thermophilic proteins to high temperatures is the presence of additional hydrogen bonds in the thermophilic proteins, which means that the structure of the protein is more resistant to unfolding. Similarly, thermostable proteins are rich in structure-stabilizing salt bridges and/or disulfide bridges. In this context, we perform multiple replica molecular dynamics simulations at different temperatures on the Aeropyrum pernix (L7Ae) protein (from the crenarchaeal species A. pernix), known for its high melting temperature, and this in the aim to elucidate the structural factors responsible for its high thermostability. The results reveal that between the most sensitive regions of the protein to the increase of temperature are the loops L1, and L5, which surround the hydrophobic core region of the protein, besides the loop L9, and the C-terminal α5 region. This latter is the longer alpha helix of the protein secondary structure motifs and it is the first to be denaturated at 450 K, while the rest of the protein secondary structure motifs at this temperature were intact. The mechanism of unfolding that follows this protein at 550 K is similar to other thermophile proteins found in literature, with the opening of the loops that surround the hydrophobic core of the protein. So, the latter is completely exposed to the solvent, and partially denatured. The total denaturation process of the protein takes an average time of 40 ns to be achieved. Our investigation also shows that all the calculated salt bridges, with distances less than or equal to 6 A°, are on the periphery part of the protein, exposed to the solvent. However, the hydrophobic core of the protein is not involved in the formation of salt bridges, but rather with formation of some important hydrogen bondings that still persist even at 450 K. So, optimizing hydrogen bonding, near or within the core region, at high temperatures is a strategy that follows this thermostable protein to protect its hydrophobic core from denaturation, and ensure the thermal stability of the protein.
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Affiliation(s)
- Djamila Benrezkallah
- Department of Basic Teachings in Sciences and Technologies (EBST), Faculty of Technology, Djillali Liabes University, Ben M'Hidi BP 89, Sidi Bel Abbes 22000, Algeria; LCPM Laboratory, Chemistry Department, Faculty of Exact and Applied Sciences, University Oran 1 Ahmed Ben Bella, El Mnaouer BP 1524, Oran 31000, Algeria.
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Zhang H, Ye YH, Wang Y, Liu JZ, Jiao QC. A Bibliometric Analysis: Current Perspectives and Potential Trends of Enzyme Thermostability from 1991-2022. Appl Biochem Biotechnol 2024; 196:1211-1240. [PMID: 37382790 DOI: 10.1007/s12010-023-04615-6] [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] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
Thermostability is considered a crucial parameter to evaluate the viability of enzymes in industrial applications. Over the past 31 years, many studies have been reported on the thermostability of enzymes. However, there is no systematic bibliometric analysis of publications on the thermostability of enzymes. In this study, 16,035 publications related to the thermostability of enzymes were searched and collected, showing an increasing annual trend. China contributed the most publications, while the United States had the highest citation count. International Journal of Biological Macromolecules is the most productive journal in the research field. Moreover, Chinese acad sci and Khosro Khajeh are the most active institutions and prolific authors in the field, respectively. Analysis of references with the strongest citation bursts and keyword co-occurrences, magnetic nanoparticles, metal-organic frameworks, molecular dynamics, and rational design are current hot spots and significant future research directions. This study is the first comprehensive bibliometric analysis summarizing trends and developments in enzyme thermostability research. Our findings could provide scholars with an understanding of the fundamental knowledge framework of the field and identify recent potential hotspots and research trends that could facilitate the discovery of collaboration opportunities.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yun-Hui Ye
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yu Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jun-Zhong Liu
- Nanjing Institute for Comprehensive Utilization of Wild Plants, CHINA CO-OP, Nanjing, 211111, China.
| | - Qing-Cai Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Gao W, Ding F, Wu J, Ma W, Wang C, Man Z, Cai Z, Guo J. Modulation of a Loop Region in the Substrate Binding Pocket Affects the Degree of Polymerization of Bacillus subtilis Chitosanase Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4358-4366. [PMID: 38349745 DOI: 10.1021/acs.jafc.3c09313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
The hydrolytic products of chitosanase from Streptomyces avermitilis (SaCsn46A) were found to be aminoglucose and chitobiose, whereas those of chitosanase from Bacillus subtilis (BsCsn46A) were chitobiose and chitotriose. Therefore, the sequence alignment between SaCsn46A and BsCsn46A was conducted, revealing that the structure of BsCsn46A possesses an extra loop region (194N-200T) at the substrate binding pocket. To clarify the impact of this loop on hydrolytic properties, three mutants, SC, TJN, and TJA, were constructed. Eventually, the experimental results indicated that SC changed the ratio of chitobiose to chitotriose hydrolyzed by chitosanase from 1:1 into 2:3, while TJA resulted in a ratio of 15:7. This experiment combined molecular research to unveil a crucial loop within the substrate binding pocket of chitosanase. It also provides an effective strategy for mutagenesis and a foundation for altering hydrolysate composition and further applications in engineering chitosanase.
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Affiliation(s)
- Wenjun Gao
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Fei Ding
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Jie Wu
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Weiqi Ma
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Chao Wang
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
| | - Zaiwei Man
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou 213164, China
| | - Zhiqiang Cai
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou 213164, China
| | - Jing Guo
- Laboratory of Applied Microbiology, School of Pharmacy, School of Biological and Food Engineering, Changzhou University, Changzhou 213164, China
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou 213164, China
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6
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Shahmoradipour P, Zaboli M, Torkzadeh-Mahani M. Exploring the impact of taurine on the biochemical properties of urate oxidase: response surface methodology and molecular dynamics simulation. J Biol Eng 2024; 18:10. [PMID: 38254151 PMCID: PMC10804793 DOI: 10.1186/s13036-023-00397-x] [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: 10/04/2023] [Accepted: 12/05/2023] [Indexed: 01/24/2024] Open
Abstract
This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy.
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Affiliation(s)
- Parisa Shahmoradipour
- Department of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Maryam Zaboli
- Department of chemistry, faculty of science, University of Birjand, Birjand, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, , Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
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7
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Muellers SN, Allen KN, Whitty A. MEnTaT: A machine-learning approach for the identification of mutations to increase protein stability. Proc Natl Acad Sci U S A 2023; 120:e2309884120. [PMID: 38039271 PMCID: PMC10710055 DOI: 10.1073/pnas.2309884120] [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: 06/12/2023] [Accepted: 10/16/2023] [Indexed: 12/03/2023] Open
Abstract
Enhancing protein thermal stability is important for biomedical and industrial applications as well as in the research laboratory. Here, we describe a simple machine-learning method which identifies amino acid substitutions that contribute to thermal stability based on comparison of the amino acid sequences of homologous proteins derived from bacteria that grow at different temperatures. A key feature of the method is that it compares the sequences based not simply on the amino acid identity, but rather on the structural and physicochemical properties of the side chain. The method accurately identified stabilizing substitutions in three well-studied systems and was validated prospectively by experimentally testing predicted stabilizing substitutions in a polyamine oxidase. In each case, the method outperformed the widely used bioinformatic consensus approach. The method can also provide insight into fundamental aspects of protein structure, for example, by identifying how many sequence positions in a given protein are relevant to temperature adaptation.
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Affiliation(s)
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA02215
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA02215
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Dehghanbanadaki N, Mehralitabar H, Sotoudeh R, Naderi-Manesh H. The role of Wnt palmitoleylated loop conserved disulfide bonds in Wnt-frizzled complex structural dynamics: Insights from molecular dynamics simulations. Comput Biol Med 2023; 167:107703. [PMID: 37979393 DOI: 10.1016/j.compbiomed.2023.107703] [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: 07/29/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023]
Abstract
Wnts are lipid-modified proteins rich in cysteine, regulating developmental processes, and are involved in various pathological conditions. Wnts structure resembles a hand, with a palmitoleylated thumb and an index finger-like domain interacting with frizzled (FZ) receptors. Previous research shows the palmitoleyl group and the disulfides importance in Wnt folding, secretion, and function, but the structural basis is not fully understood. Here, we utilized classical molecular dynamics simulation (800-ns in total) to investigate how the thumb palmitoleyl and its close conserved disulfides (183-190, 181-195) regulated Wnt-FZ interaction and structural dynamics. Using Steered molecular dynamics experiment followed by a relaxing procedure, we also explored if these disulfides are important in Wnt-FZ complex formation. According to our results, the palmitoleyl group contributes significantly to stabilize Wnt-FZ interaction, and the disulfides modulate this contribution. We also demonstrated that disulfide 183-190 regulates the Wnt thumb fluctuation, hydrogen bond network, and secondary structure. The DCCM analysis depicted disulfide 183-190 roles in regulating native-like collective movement in the palmitoleylated loop, which changed after this disulfide removal. The pulling-relaxing experiment showed that both the disulfides, and especially, the disulfide 183-190, are highly important for long-range salt-bridge interaction establishment between Wnt Lys182 and FZ Glu64, led palmitoleyl group appropriate positioning to FZ, suggested this disulfide essential role in Wnt-FZ complex formation. Together, our findings provide new insights to how thumb-positioned disulfides contribute to Wnt-FZ complex formation, structural dynamics, and stability, introducing disulfide 183-190 as a consequential element to target in drug design and development against Wnt signalling.
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Affiliation(s)
- N Dehghanbanadaki
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran
| | - H Mehralitabar
- Department of Basic Sciences, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, PO Box. 48181 68984, Sari, Iran
| | - R Sotoudeh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran
| | - H Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, PO Box: 14115-154, Tehran, Iran.
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Komp E, Alanzi HN, Francis R, Vuong C, Roberts L, Mosallanejad A, Beck DAC. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023; 10:682. [PMID: 37805601 PMCID: PMC10560248 DOI: 10.1038/s41597-023-02553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
Stability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Humood N Alanzi
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Ryan Francis
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Chau Vuong
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Logan Roberts
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Amin Mosallanejad
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
- Paul G. Allen School of Computer Science, University of Washington, Seattle, USA.
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Xie CY, Li WJ, Feng H. Tuning transcription factor DegU for developing extracellular protease overproducer in Bacillus pumilus. Microb Cell Fact 2023; 22:163. [PMID: 37635205 PMCID: PMC10464342 DOI: 10.1186/s12934-023-02177-0] [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: 05/24/2023] [Accepted: 08/11/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Global transcription machinery engineering (gTME) is an effective approach employed in strain engineering to rewire gene expression and reshape cellular metabolic fluxes at the transcriptional level. RESULTS In this study, we utilized gTME to engineer the positive transcription factor, DegU, in the regulation network of major alkaline protease, AprE, in Bacillus pumilus. To validate its functionality when incorporated into the chromosome, we performed several experiments. First, three negative transcription factors, SinR, Hpr, and AbrB, were deleted to promote AprE synthesis. Second, several hyper-active DegU mutants, designated as DegU(hy), were selected using the fluorescence colorimetric method with the host of the Bacillus subtilis ΔdegSU mutant. Third, we integrated a screened degU(L113F) sequence into the chromosome of the Δhpr mutant of B. pumilus SCU11 to replace the original degU gene using a CRISPR/Cas9 system. Finally, based on transcriptomic and molecular dynamic analysis, we interpreted the possible mechanism of high-yielding and found that the strain produced alkaline proteases 2.7 times higher than that of the control strain (B. pumilus SCU11) in LB medium. CONCLUSION Our findings serve as a proof-of-concept that tuning the global regulator is feasible and crucial for improving the production performance of B. pumilus. Additionally, our study established a paradigm for gene function research in strains that are difficult to handle.
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Affiliation(s)
- Chao-Ying Xie
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Wen-Jin Li
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Hong Feng
- Key Laboratory for Bio-resources and Eco-Environment of the Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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Omar SI, Keasar C, Ben-Sasson AJ, Haber E. Protein Design Using Physics Informed Neural Networks. Biomolecules 2023; 13:biom13030457. [PMID: 36979392 PMCID: PMC10046838 DOI: 10.3390/biom13030457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
The inverse protein folding problem, also known as protein sequence design, seeks to predict an amino acid sequence that folds into a specific structure and performs a specific function. Recent advancements in machine learning techniques have been successful in generating functional sequences, outperforming previous energy function-based methods. However, these machine learning methods are limited in their interoperability and robustness, especially when designing proteins that must function under non-ambient conditions, such as high temperature, extreme pH, or in various ionic solvents. To address this issue, we propose a new Physics-Informed Neural Networks (PINNs)-based protein sequence design approach. Our approach combines all-atom molecular dynamics simulations, a PINNs MD surrogate model, and a relaxation of binary programming to solve the protein design task while optimizing both energy and the structural stability of proteins. We demonstrate the effectiveness of our design framework in designing proteins that can function under non-ambient conditions.
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Affiliation(s)
| | - Chen Keasar
- Department of Computer Science, Ben Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Ariel J. Ben-Sasson
- Independent Researcher, Haifa 3436301, Israel
- Correspondence: (A.J.B.-S.); (E.H.)
| | - Eldad Haber
- Department of Earth Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Correspondence: (A.J.B.-S.); (E.H.)
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12
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Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
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Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
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Azemin WA, Alias N, Ali AM, Shamsir MS. Structural and functional characterisation of HepTH1-5 peptide as a potential hepcidin replacement. J Biomol Struct Dyn 2023; 41:681-704. [PMID: 34870559 DOI: 10.1080/07391102.2021.2011415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepcidin is a principal regulator of iron homeostasis and its dysregulation has been recognised as a causative factor in cancers and iron disorders. The strategy of manipulating the presence of hepcidin peptide has been used for cancer treatment. However, this has demonstrated poor efficiency and has been short-lived in patients. Many studies reported using minihepcidin therapy as an alternative way to treat hepcidin dysregulation, but this was only applied to non-cancer patients. Highly conserved fish hepcidin protein, HepTH1-5, was investigated to determine its potential use in developing a hepcidin replacement for human hepcidin (Hepc25) and as a therapeutic agent by targeting the tumour suppressor protein, p53, through structure-function analysis. The authors found that HepTH1-5 is stably bound to ferroportin, compared to Hepc25, by triggering the ferroportin internalisation via Lys42 and Lys270 ubiquitination, in a similar manner to the Hepc25 activity. Moreover, the residues Ile24 and Gly24, along with copper and zinc ligands, interacted with similar residues, Lys24 and Asp1 of Hepc25, respectively, showing that those molecules are crucial to the hepcidin replacement strategy. HepTH1-5 interacts with p53 and activates its function through phosphorylation. This finding shows that HepTH1-5 might be involved in the apoptosis signalling pathway upon a DNA damage response. This study will be very helpful for understanding the mechanism of the hepcidin replacement and providing insights into the HepTH1-5 peptide as a new target for hepcidin and cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia.,Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nadiawati Alias
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Abdul Manaf Ali
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
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14
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Rational engineering of a metalloprotease to enhance thermostability and activity. Enzyme Microb Technol 2023; 162:110123. [DOI: 10.1016/j.enzmictec.2022.110123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022]
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15
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Patel S, Patel A, Nair A, Shah K, Shah K, Tanavde V, Rawal R. Salinomycin mediated therapeutic targeting of circulating stem like cell population in oral cancer. J Biomol Struct Dyn 2022; 40:11141-11153. [PMID: 34308783 DOI: 10.1080/07391102.2021.1957018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CD44+ circulating tumor stem cells (CTSCs) have been significantly associated with aggressiveness, resistance and poor prognosis of oral cancer patients. Thus, targeted elimination of these CTSCs could be a new conceptual framework for enhancing the therapeutic outcome of patients. Docking of potential investigational molecules and simulation results identified Salinomycin as a potential lead compound that could effectively inhibit CD44 receptor. To assess the cytotoxic effect, immuno-magnetically sorted circulatory CD44+ cells were subjected to increasing concentrations of 5FU, Cisplatin and Salinomycin. Salinomycin demonstrated significant cytotoxic effect towards the CD44+ subpopulation in a dose and time dependent manner. Further the effect of these compounds was investigated on apoptosis, cell cycle, signaling pathways and gene expression profiles using MuseTM flow cytometer and Real-Time PCR. It was observed that mRNA expression patterns of CD44v6, Nanog, AKT1, CDKN2A and β-catenin of Salinomycin treated CD44+ cells. Moreover, Salinomycin significantly induced programmed cell death by inducing G2/M cell cycle arrest and inhibiting MAPK/PI3K pathways in this chemo-resistant population. Thus, this study demonstrated the potential of Salinomycin to target the chemo-resistant circulating CD44 population by attenuating its proliferation and survival.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shanaya Patel
- Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Aditi Patel
- Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Aishwarya Nair
- Biological & Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat, India
| | - Kavan Shah
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Kanisha Shah
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Vivek Tanavde
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Rakesh Rawal
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
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16
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Roy A, Gauld JW. Molecular Dynamics Investigation on the Effects of Protonation and Lysyl Hydroxylation on Sulfilimine Cross-links in Collagen IV. ACS OMEGA 2022; 7:39680-39689. [PMID: 36385809 PMCID: PMC9647856 DOI: 10.1021/acsomega.2c03360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Collagen IV networks are an essential component of basement membranes that are important for their structural integrity and thus that of an organism's tissues. Improper functioning of these networks has been associated with several diseases. Cross-links, such as sulfilimine bonds interconnecting NC1 domains, are critical for forming and mechanically stabilizing these collagen IV networks. More specifically, the sulfilimine cross-links form between methionine (Met93) and lysine/hydroxylsine (Lys211/Hyl211) residues of NC1 domains. Therefore, the dynamic nature of the sulfilimine bond in collagen IV is crucial for network formation. To understand the dynamic nature of a neutral and protonated sulfilimine bond in collagen IV, we performed molecular dynamics (MD) simulations on four sulfilimine cross-linked systems (i.e., Met93S-NLys211, Met93S-NHLys211 +, Met93S-NHyl211, and Met93S-NHHyl211 +) of collagen IV. The MD results showed that the neutral Met93S-NLys211 system has the smallest protein backbone and showed the cross-linked residues' RMSD value. The conformational change analyses showed that the conformations of the sulfilimine cross-linked residues take on a U-shape for the Met93S-NHyl211 and Met93S-HNHyl211 + systems, whereas the conformations of the sulfilimine cross-linked residues are more open for the Met93S-NLys211, and Met93S-NHLys211 + systems. Protonation is a crucial biochemical process to stabilize the protein structure or the biological cross-links. Furthermore, the protonation of the sulfilimine bond could potentially influence hydrogen bond interaction with near amino acid residues, and according to water distribution analyses, the sulfilimine bond can potentially exist in one or more protonation states.
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17
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Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:molecules27206861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
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18
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Immunoinformatics-Based Proteome Mining to Develop a Next-Generation Vaccine Design against Borrelia burgdorferi: The Cause of Lyme Borreliosis. Vaccines (Basel) 2022; 10:vaccines10081239. [PMID: 36016127 PMCID: PMC9414436 DOI: 10.3390/vaccines10081239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 02/08/2023] Open
Abstract
The tick-borne bacterium, Borrelia burgdorferi has been implicated in Lyme disease-a deadly infection, formerly confined to North America, but currently widespread across Europe and Asia. Despite the severity of this disease, there is still no human Lyme disease vaccine available. A reliable immunoinformatic approach is urgently needed for designing a therapeutic vaccine against this Gram-negative pathogen. Through this research, we explored the immunodominant proteins of B. burgdorferi and developed a novel and reliable vaccine design with great immunological predictability as well as low contamination and autoimmunity risks. Our initial analysis involved proteome-wide analysis to filter out proteins on the basis of their redundancy, homology to humans, virulence, immunogenicity, and size. Following the selection of proteins, immunoinformatic tools were employed to identify MHC class I & II epitopes and B-cell epitopes, which were subsequently subjected to a rigorous screening procedure. In the final formulation, ten common MHC-I and II epitopes were used together with a suitable adjuvant. We predicted that the final chimeric multi-epitope vaccine could invoke B-cell responses and IFN-gamma-mediated immunity as well as being stable and non-allergenic. The dynamics simulations predicted the stable folding of the designed molecule, after which the molecular docking predicted the stability of the interaction between the potential antigenic epitopes and human immune receptors. Our studies have shown that the designed next-generation vaccine stimulates desirable immune responses, thus potentially providing a viable way to prevent Lyme disease. Nevertheless, further experimental studies in a wet lab are needed in order to validate the results.
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19
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Rahban M, Zolghadri S, Salehi N, Ahmad F, Haertlé T, Rezaei-Ghaleh N, Sawyer L, Saboury AA. Thermal stability enhancement: Fundamental concepts of protein engineering strategies to manipulate the flexible structure. Int J Biol Macromol 2022; 214:642-654. [DOI: 10.1016/j.ijbiomac.2022.06.154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/28/2023]
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20
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Qu Y, Davey K, Sun Y, Middelberg A, Bi J. Engineered Design of the E-Helix Structure on Ferritin Nanoparticles. ACS APPLIED BIO MATERIALS 2022; 5:3167-3179. [PMID: 35770389 DOI: 10.1021/acsabm.2c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Insertion of an immunogenic epitope at the C-terminus of ferritin has shown the potential to produce a stable and efficacious vaccine. There is however limited understanding of how C-terminus insertion affects ferritin protein stability. The E-helix at the C-terminus has attracted interest because there are contradictory reports as to whether it has a role in protein stabilization. Here, we report, for the first time, combining molecular dynamics simulation (MDS) with experiment to engineer the design of the E-helix at the C-terminus of engineered human ferritin heavy chain (F1) inserted with Epstein-Barr nuclear antigen 1 (EBNA1, E1) and flexible linker (L3) residues (to afford F1L3E1). Hot spots on the E-helix of the C-terminus were predicted by MDS at aa 167 (Glu) and aa 171 (Asp). Five (5) variants of F1L3E1 were constructed by considering hot spots and alteration of electrostatic or hydrophobic interfaces, namely, (1) C1, hot spots substituted with noncharged residue Gln; (2) C2, hot spots substituted with positively charged residue Arg; (3) C3, hydrophobic residues substituted with the most hydrophobic residues Val and Ile; (4) C4, hydrophobic residues substituted with the most hydrophilic residues Gln and Asn; and (5) C5, a heptad repeat structure in the E-helix disrupted by substituting "a" and "d" heptad residues with noncharged polar residue Gln. It was found that the E-helix is essential to maintain integrated protein stability and that changing the hydrophobic interface (C3 and C4) had more significant effects on protein folding and stability than changing the electrostatic interface (C1 and C2). It was confirmed by both MDS and experiment that variants C1, C2, and C5 were able to fold to form stable conformational structures with protein surface hydrophobicity similar to that of F1L3E1. However, they are less thermally stable than F1L3E1. Significant changes in hydrophobicity drove significant protein aggregation for variants C3 and C4. It is concluded that the molecular design of the C-terminus in engineered ferritin, especially the E-helix, is important to ensure the epitope-based chimeric vaccine is safe (aggregate free) and efficacious.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kenneth Davey
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- Division of Research and Innovation, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
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21
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Discovery of a New Microbial Origin Cold-Active Neopullulanase Capable for Effective Conversion of Pullulan to Panose. Int J Mol Sci 2022; 23:ijms23136928. [PMID: 35805929 PMCID: PMC9267027 DOI: 10.3390/ijms23136928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Panose is a type of functional sugar with diverse bioactivities. The enzymatic conversion bioprocess to produce high purity panose with high efficiency has become increasingly important. Here, a new neopullulanase (NPase), Amy117 from B. pseudofirmus 703, was identified and characterized. Amy117 presented the optimal activity at pH 7.0 and 30 °C, its activity is over 40% at 10 °C and over 80% at 20 °C, which is cold-active. The enzyme cleaved α-1, 4-glycosidic linkages of pullulan to generate panose as the only hydrolysis product, and degraded cyclodextrins (CDs) and starch to glucose and maltose, with an apparent preference for CDs. Furthermore, Amy117 can produce 72.7 mg/mL panose with a conversion yield of 91% (w/w) based on 80 mg/mL pullulan. The sequence and structure analysis showed that the low proportion of Arg, high proportion of Asn and Gln, and high α-helix levels in Amy117 may contribute to its cold-active properties. Root mean square deviation (RMSD) analysis also showed that Amy117 is more flexible than two mesophilic homologues. Hence, we discovered a new high-efficiency panose-producing NPase, which so far achieves the highest panose production and would be an ideal candidate in the food industry.
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22
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Ray S, Luharuka S. Mutational Analysis of Interleukin-11 and its Consequences on Cancer and
COVID-19 Related Cytokine Storm -An Extensive Molecular Dynamics
Study. Protein Pept Lett 2022; 29:514-537. [DOI: 10.2174/0929866529666220405102230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/07/2021] [Accepted: 12/25/2021] [Indexed: 11/22/2022]
Abstract
Background:
Interleukin-11 is a pleiotropic cytokine that is known to play an important
role in the progression of various forms of cancer by modulating the survival and proliferation of
tumour cells. IL11 also demonstrates a structural homology to IL6, the predominant cytokine
involved in COVID-19. This makes IL11 a potential therapeutic target in both diseases.
Objective:
This study aimed to evaluate the impact of the two-point mutations, R135E and R190E,
on the stability of IL11 and their effect on the binding affinity of IL11 with its receptor IL11Rα. It is
a molecular level analysis based on the existing experimental validation.
Method:
Computer-aided drug designing techniques, such as molecular modelling, molecular
docking, and molecular dynamics simulations, were employed to determine the consequential
effects of the two-point mutations.
Results:
Our analysis revealed that the two mutations led to a decrease in the overall stability of
IL11. This was evident by the increased atomic fluctuations in the mutated regions as well as the
corresponding elevation in the deviations seen through RMSD and Rg values. It was also
accompanied by a loss in the secondary structural organisation in the mutated proteins. Moreover,
mutation R135E led to an increase in the binding affinity of IL11 with IL11Rα and the formation of
a more stable complex in comparison to the wild-type protein with its receptor.
CONCLUSION:
Mutation R190E led to the formation of a less stable complex than the wild-type,
which suggests a decrease in the binding affinity between IL11 and IL11Rα.
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Affiliation(s)
- Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Shreya Luharuka
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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23
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Nguyen C, Yearwood LM, McCully ME. Thermostabilization mechanisms in thermophilic versus mesophilic three-helix bundle proteins. J Comput Chem 2022; 43:197-205. [PMID: 34738662 PMCID: PMC8665064 DOI: 10.1002/jcc.26782] [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: 03/17/2021] [Revised: 07/22/2021] [Accepted: 10/24/2021] [Indexed: 11/21/2022]
Abstract
The engineered three‐helix bundle, UVF, is thermostabilized entropically due to heightened, native‐state dynamics. However, it is unclear whether this thermostabilization strategy is observed in natural proteins from thermophiles. We performed all‐atom, explicit solvent molecular dynamics simulations of two three‐helix bundles from thermophilic H. butylicus (2lvsN and 2lvsC) and compared their dynamics to a mesophilic three‐helix bundle, the Engrailed homeodomain (EnHD). Like UVF, 2lvsC had heightened native dynamics, which it maintained without unfolding at 100°C. Shortening and rigidification of loops in 2lvsN and 2lvsC and increased surface hydrogen bonds in 2lvsN were observed, as is common in thermophilic proteins. A buried disulfide and salt bridge in 2lvsN and 2lvsC, respectively, provided some stabilization, and addition of a homologous disulfide bond in EnHD slowed unfolding. The transferability and commonality of stabilization strategies among members of the three‐helix bundle fold suggest that these strategies may be general and deployable in designing thermostable proteins.
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Affiliation(s)
- Catrina Nguyen
- Department of Biology, Santa Clara University, Santa Clara, California, USA
| | - Lauren M Yearwood
- Department of Biology, Santa Clara University, Santa Clara, California, USA
| | - Michelle E McCully
- Department of Biology, Santa Clara University, Santa Clara, California, USA
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Santos SP, Lisboa AB, Silva FS, Tiwari S, Azevedo V, Cruz ÁA, Silva ES, Pinheiro CS, Alcantara-Neves NM, Pacheco LG. Rationally designed hypoallergenic mutant variants of the house dust mite allergen Der p 21. Biochim Biophys Acta Gen Subj 2022; 1866:130096. [DOI: 10.1016/j.bbagen.2022.130096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/22/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
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Immunoinformatics guided design of a next generation epitope-based vaccine against Kaposi Sarcoma. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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26
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Ranjan P, Das P. Understanding the impact of missense mutations on the structure and function of the EDA gene in X-linked hypohidrotic ectodermal dysplasia: A bioinformatics approach. J Cell Biochem 2021; 123:431-449. [PMID: 34817077 DOI: 10.1002/jcb.30186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022]
Abstract
X-linked hypohidrotic dysplasia (XLHED), caused by mutations in the EDA gene, is a rare genetic disease that affects the development and function of the teeth, hair, nails, and sweat glands. The structural and functional consequences of caused by an ectodysplasin-A (EDA) mutations on protein phenotype, stability, and posttranslational modifications (PTMs) have not been well investigated. The present investigation involves five missense mutations that cause XLHED (L56P, R155C, P220L, V251M, and V322A) in different domains of EDA (TM, furin, collagen, and tumor necrosis factor [TNF]) from previously published papers. The deleterious nature of EDA mutant variants was identified using several computational algorithm tools. The point mutations induce major drifts in the structural flexibility of EDA mutant variants and have a negative impact on their stability, according to the 3D protein modeling tool assay. Using the molecular docking technique, EDA/EDA variants were docked to 10 EDA interacting partners, retrieved from the STRING database. We found a novel biomarker CD68 by molecular docking analysis, suggesting all five EDA variants had lower affinity for EDAR, EDA2R, and CD68, implying that they would affect embryonic signaling between the ectodermal and mesodermal cell layers. In silico research such as gene ontology, subcellular localization, protein-protein interaction, and PTMs investigations indicates major functional alterations would occur in EDA variants. According to molecular simulations, EDA variants influence the structural conformation, compactness, stiffness, and function of the EDA protein. Further studies on cell line and animal models might be useful in determining their specific roles in functional annotations.
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Affiliation(s)
- Prashant Ranjan
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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27
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Guo J, Wang Y, Zhang X, Gao W, Cai Z, Hong T, Man Z, Qing Q. Improvement of the Catalytic Activity of Chitosanase BsCsn46A from Bacillus subtilis by Site-Saturation Mutagenesis of Proline121. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11835-11846. [PMID: 34590486 DOI: 10.1021/acs.jafc.1c04206] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
BsCsn46A, a GH46 family chitosanase from Bacillus subtilis, has great potential for industrial chitooligosaccharide production due to its high activity and stability. In this study, a special amino acid Pro121 was identified not fit in the helix structure, which was located in the opposite side of the active center in BsCsn46A, by the PoPMuSiC algorithm. Then, saturation mutagenesis was performed to explore the role of the site amino acid 121. Compared with the wild type, the specific activity of P121N, P121C, and P121V was increased by 1.69-, 1.97-, and 2.15-fold, respectively. In particular, the specific activity of P121N was increased without loss of thermostability, indicating that replacing the structural stiffness of proline in the helical structure could significantly improve the chitosanase activity. The Km values of P121N, P121C, and P121V decreased significantly, indicating that the affinity between the enzyme-substrate complex was enhanced. Through molecular docking, it was found that the increase of hydrogen bonds and van der Waals force between the enzyme-substrate complex and the removal of unfavorable bonds might be the main reason for the change of enzyme properties. In addition, the optimal temperature of the three mutants changed from 60 to 55 °C. These results indicate that the site 121 plays a critical role in the catalytic activity and enzymatic properties of chitosanase. To our knowledge, the results provide novel data on chitosanase activity and identify an excellent candidate of industrial chitosanase.
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Affiliation(s)
- Jing Guo
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, Jiangsu 213164, China
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Yi Wang
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Xuan Zhang
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Wenjun Gao
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Zhiqiang Cai
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, Jiangsu 213164, China
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Tingting Hong
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, Jiangsu 213164, China
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
| | - Zaiwei Man
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, Jiangsu 213164, China
- School of Petrochemical Engineering, School of food Science and Technology, Changzhou University, Changzhou, Jiangsu 213164, China
- Zaozhuang Key Laboratory of Corn Bioengineering, Zaozhuang Science and Technology Collaborative Innovation Center of Enzyme, Shandong Hengren Gongmao Co. Ltd, Zaozhuang 277100, China
| | - Qing Qing
- Advanced Catalysis and Green Manufacturing Collaborative Innovation Center, Changzhou University, Changzhou, Jiangsu 213164, China
- Laboratory of Applied Microbiology, School of Pharmaceutical, Changzhou University, Changzhou 213164, Jiangsu, China
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Jovanović JĐ, Antonijević M, El‐Emam AA, Marković Z. Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M pro. ChemistrySelect 2021; 6:8603-8610. [PMID: 34909459 PMCID: PMC8662094 DOI: 10.1002/slct.202101898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022]
Abstract
In this study, the inhibitory potency of four adamantly- isothiourea derivatives (compounds 1 [4-bromobenzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 2 [3,5-bis(trifluoromethyl)benzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 3 [4-bromobenzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate] and 4 [3,5-bis(trifluoromethyl)benzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate]) was evaluated against SARS-CoV-2 targeted proteins. The investigated compounds 1-4 possess a similar structure to opaganib, which is used in studies like a potential drug for COVID-19 treatment. Since examined adamantly-isothiourea derivatives (1-4) shown broad-spectrum of antibacterial activity and significant in vitro cytotoxic effects against five human tumor cell lines and shown similarity in structure with opaganib, it was of interest to study their inhibitory potency toward some SARS-CoV-2 proteins such as SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G. The inhibitory potency of studied compounds is examined using molecular docking and molecular dynamic simulations. The results of molecular docking simulations indicate compound 1 as the most prominent candidate of inhibition of SARS-CoV-2 main protease Mpro (▵Gbind=11.24 kcal/mol), while almost the same inhibition potency of all studied compounds is exhibited toward D614G. Regarding the results obtained by molecular dynamic simulations, compounds 1 and 4 possess similar inhibitory potency toward SARS-CoV-2 main protease Mpro as opaganib (▵Gbind ≈ 40 kcal/mol).
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Affiliation(s)
- Jelena Đorović Jovanović
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Marko Antonijević
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Ali A. El‐Emam
- Department of Medicinal ChemistryFaculty of PharmacyMansoura UniversityMansoura35516Egypt
| | - Zoran Marković
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
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Poghosyan AH, Shahinyan AA, Kirakosyan GR, Ayvazyan NM, Mamasakhlisov YS, Papoian GA. A molecular dynamics study of protein denaturation induced by sulfonate-based surfactants. J Mol Model 2021; 27:261. [PMID: 34432183 DOI: 10.1007/s00894-021-04882-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Microsecond timescale explicit-solvent atomistic simulations were carried out to investigate how anionic surfactants modulate protein structure and dynamics. We found that lysozyme undergoes near-complete denaturation at the high concentration (> 0.1 M) of sodium pentadecyl sulfonate (SPDS), while only partial denaturation occurs at the concentration slightly below 0.1 M. In large part, protein denaturation is structurally manifested by disappearance of helical segments and loss of tertiary interactions. The computational prediction of the extent of burial of cysteine residues was experimentally validated by measuring the accessibility of the respective sulfhydryl groups. Overall, our work indicates an interesting synergy between electrostatic and hydrophobic contributions to lysozyme's denaturation process by anionic surfactants. In fact, first disulfide bridges and hydrogen bonds from protein surface to SPDS head groups loosen the protein globule followed by fuller denaturation via insertion of the surfactant's hydrophobic tails into the protein core.
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Affiliation(s)
- Armen H Poghosyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia.
| | - Aram A Shahinyan
- The International Scientific-Educational Center of NAS RA, M. Baghramyan 24d, 0019, Yerevan, Armenia
| | - Gayane R Kirakosyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | - Naira M Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbely str. 22, 0019, Yerevan, Armenia
| | | | - Garegin A Papoian
- Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
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Ardila-Leal LD, Monterey-Gutiérrez PA, Poutou-Piñales RA, Quevedo-Hidalgo BE, Galindo JF, Pedroza-Rodríguez AM. Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study. BMC Biotechnol 2021; 21:37. [PMID: 34088291 PMCID: PMC8178886 DOI: 10.1186/s12896-021-00698-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Laccases (EC 1.10.3.2) are multi-copper oxidoreductases with great biotechnological importance due to their high oxidative potential and utility for removing synthetic dyes, oxidizing phenolic compounds, and degrading pesticides, among others. Methods A real-time stability study (RTS) was conducted for a year, by using enzyme concentrates from 3 batches (L1, L3, and L4). For which, five temperatures 243.15, 277.15, 298.15, 303.15, 308.15, and 313.15 K were assayed. Using RTS data and the Arrhenius equation, we calculated the rPOXA 1B accelerated stability (AS). Molecular dynamics (MD) computational study results were very close to those obtained experimentally at four different temperatures 241, 278, 298, and 314 K. Results In the RTS, 101.16, 115.81, 75.23, 46.09, 5.81, and 4.83% of the relative enzyme activity were recovered, at respective assayed temperatures. AS study, showed that rPOXA 1B is stable at 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K; with t1/2 values of 230.8, 46.2, and 12.6 months, respectively. Kinetic and thermodynamic parameters supported the high stability of rPOXA 1B, with an Ed value of 41.40 KJ mol− 1, a low variation of KM and Vmax, at 240.98 ± 5.38, and 297.53 ± 3.88 K, and ∆G values showing deactivation reaction does not occur. The MD indicates that fluctuations in loop, coils or loops with hydrophilic or intermediate polarity amino acids as well as in some residues of POXA 1B 3D structure, increases with temperature; changing from three fluctuating residues at 278 K to six residues at 298 K, and nine residues at 314 K. Conclusions Laccase rPOXA 1B demonstrated experimentally and computationally to be a stable enzyme, with t1/2 of 230.8, 46.2 or 12.6 months, if it is preserved impure without preservatives at temperatures of 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K respectively; this study could be of great utility for large scale producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00698-3.
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Affiliation(s)
- Leidy D Ardila-Leal
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
| | - Pedro A Monterey-Gutiérrez
- Vicerrectoría Académica. Universidad Antonio Nariño, Programa de Maestría y Doctorado en Educación Matemática, Bogotá, D.C, Colombia
| | - Raúl A Poutou-Piñales
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Balkys E Quevedo-Hidalgo
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ), Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Johan F Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
| | - Aura M Pedroza-Rodríguez
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
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Arnittali M, Rissanou AN, Amprazi M, Kokkinidis M, Harmandaris V. Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments. Int J Mol Sci 2021; 22:ijms22115931. [PMID: 34073028 PMCID: PMC8199364 DOI: 10.3390/ijms22115931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023] Open
Abstract
In the current work we study, via molecular simulations and experiments, the folding and stability of proteins from the tertiary motif of 4-α-helical bundles, a recurrent motif consisting of four amphipathic α-helices packed in a parallel or antiparallel fashion. The focus is on the role of the loop region in the structure and the properties of the wild-type Rop (wtRop) and RM6 proteins, exploring the key factors which can affect them, through all-atom molecular dynamics (MD) simulations and supporting by experimental findings. A detailed investigation of structural and conformational properties of wtRop and its RM6 loopless mutation is presented, which display different physical characteristics even in their native states. Then, the thermal stability of both proteins is explored showing RM6 as more thermostable than wtRop through all studied measures. Deviations from native structures are detected mostly in tails and loop regions and most flexible residues are indicated. Decrease of hydrogen bonds with the increase of temperature is observed, as well as reduction of hydrophobic contacts in both proteins. Experimental data from circular dichroism spectroscopy (CD), are also presented, highlighting the effect of temperature on the structural integrity of wtRop and RM6. The central goal of this study is to explore on the atomic level how a protein mutation can cause major changes in its physical properties, like its structural stability.
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Affiliation(s)
- Maria Arnittali
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
| | - Anastassia N. Rissanou
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Correspondence: ; Tel.: +30-2810-393746
| | - Maria Amprazi
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Department of Biology, University of Crete, GR-71409 Heraklion, Crete, Greece; (M.A.); (M.K.)
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Crete, Greece
| | - Vagelis Harmandaris
- Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Crete, Greece; (M.A.); (V.H.)
- Department of Mathematics and Applied Mathematics, University of Crete, GR-71409 Heraklion, Crete, Greece
- Computation-Based Science and Technology Research Center, The Cyprus Institute, 2121 Nicosia, Cyprus
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Alves KMA, Cardoso FJB, Honorio KM, de Molfetta FA. Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of <i>Leishmania mexicana</i>. Med Chem 2021; 16:784-795. [PMID: 31309897 DOI: 10.2174/1573406415666190712111139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. OBJECTIVE The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). METHODS A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. RESULTS Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. CONCLUSION The use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.
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Affiliation(s)
- Krisnna M A Alves
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Fábio José Bonfim Cardoso
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
| | - Kathia M Honorio
- Escola de Artes, Ciencias e Humanidades, Universidade de Sao Paulo (USP), 03828-000, Sao Paulo, SP, Brazil.,Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fábio A de Molfetta
- Laboratorio de Modelagem Molecular, Instituto de Ciencias Exatas e Naturais, Universidade Federal do Para, CP 11101, 60075-110, Belem, PA, Brazil
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Qu Y, Wang L, Yin S, Zhang B, Jiao Y, Sun Y, Middelberg A, Bi J. Stability of Engineered Ferritin Nanovaccines Investigated by Combined Molecular Simulation and Experiments. J Phys Chem B 2021; 125:3830-3842. [PMID: 33825471 DOI: 10.1021/acs.jpcb.1c00276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human ferritin is regarded as an attractive and promising vaccine platform because of its uniform structure, good plasticity, and desirable thermal and chemical stabilities. Besides, it is biocompatible and presumed safe when used as a vaccine carrier. However, there is a lack of knowledge of how different antigen insertion sites on the ferritin nanocage impact the resulting protein stability and performance. To address this question, we selected Epstein-Barr nuclear antigen 1 as a model epitope and fused it at the DNA level with different insertion sites, namely, the N- and C-termini of ferritin, to engineer proteins E1F1 and F1E1, respectively. Protein properties including hydrophobicity and thermal, pH, and chemical stability were investigated both by molecular dynamics (MD) simulation and by experiments. Both methods demonstrate that the insertion site plays an important role in protein properties. The C-terminus insertion (F1E1) leads to a less hydrophobic surface and more tolerance to the external influence of high temperature, pH, and high concentration of chemical denaturants compared to N-terminus insertion (E1F1). Simulated protein hydrophobicity and thermal stability by MD were in high accordance with experimental results. Thus, MD simulation can be used as a valuable tool to engineer nanovaccine candidates, cutting down costs by reducing the experimental effort and accelerating vaccine design.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lijie Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shuang Yin
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bingyang Zhang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Jiao
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Rasool N, Hussain W. Three Major Phosphoacceptor Sites in HIV-1 Capsid Protein Enhances its Structural Stability and Resistance Against the Inhibitor: Explication Through Molecular Dynamics Simulation, Molecular Docking and DFT Analysis. Comb Chem High Throughput Screen 2021; 23:41-54. [PMID: 31838993 DOI: 10.2174/1386207323666191213142223] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/21/2019] [Accepted: 12/07/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Human Immunodeficiency Virus 1 (HIV-1) is a lentivirus, which causes various HIV-associated infections. The HIV-1 core dissociation is essential for viral cDNA synthesis and phosphorylation of HIV-1 capsid protein (HIV-1 CA) plays an important role in it. OBJECTIVE The aim of this study was to explicate the role of three phosphoserine sites i.e. Ser109, Ser149 and Ser178 in the structural stability of HIV-1 CA, and it's binding with GS-CA1, a novel potent inhibitor. METHODS Eight complexes were analyzed and Molecular Dynamics (MD) simulations were performed to observe the stability of HIV-1 CA in the presence and absence of phosphorylation of serine residues at four different temperatures i.e. 300K, 325K, 340K and 350K, along with molecular docking and DFT analysis. RESULTS The structures showed maximum stability in the presence of phosphorylated serine residue. However, GS-CA1 docked most strongly with the native structure of HIV-1 CA i.e. binding affinity was -8.5 kcal/mol (Ki = 0.579 µM). CONCLUSION These results suggest that the phosphorylation of these three serine residues weakens the binding of GS-CA1 with CA and casts derogatory effect on inhibition potential of this inhibitor, but it supports the stability of HIV-1 CA structure that can enhance regulation and replication of HIV-1 in host cells.
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Affiliation(s)
- Nouman Rasool
- Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Waqar Hussain
- National Center of Artificial Intelligence, Punjab University College of Information Technology, University of the Punjab, Lahore, Pakistan
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Structural insights into xylanase mutant 254RL1 for improved activity and lower pH optimum. Enzyme Microb Technol 2021; 147:109786. [PMID: 33992408 DOI: 10.1016/j.enzmictec.2021.109786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/24/2022]
Abstract
Xylanases degrade xylan to valuable end products. In our previous study, the alkaline xylanase S7-xyl from Bacillus halodurans S7 was engineered by rational design and the best mutant xylanase 254RL1 exhibited 3.4-fold improvements in specific activity at pH 9.0. Further research found that the enzyme activity at pH 6.0 was almost 2-fold than that at pH 9.0. To elucidate the reason of enhanced performance of 254RL1 at decreased pH optimum, we determined the X-ray crystal structure of 254RL1 at 2.21 Å resolution. The structural analysis revealed that the mutations enlarged the opening of the access tunnel and shortened the tunnel. Moreover, the mutations changed the hydrogen bond network around the catalytic residue and decreased the pKa value of acid-base catalyst E159 which reduced the pH optimum of the xylanase. The result provided the basis for the acid-alkaline engineering of the glycoside hydrolases.
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Zaboli M, Saeidnia F, Zaboli M, Torkzadeh-Mahani M. Stabilization of recombinant d-Lactate dehydrogenase enzyme with trehalose: Response surface methodology and molecular dynamics simulation study. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sanjeev BS, Chitara D. Big Data over Cloud: Enabling Drug Design Under Cellular Environment. BIG DATA ANALYTICS 2021. [DOI: 10.1007/978-3-030-93620-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Zhou Z, Yang Z, Ou J, Zhang H, Zhang Q, Dong M, Zhang G. Temperature dependence of the SARS-CoV-2 affinity to human ACE2 determines COVID-19 progression and clinical outcome. Comput Struct Biotechnol J 2020; 19:161-167. [PMID: 33343834 PMCID: PMC7738279 DOI: 10.1016/j.csbj.2020.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 12/24/2022] Open
Abstract
The SARS-CoV-2 virus and its homolog SARS-CoV penetrate human cells by binding of viral spike protein and human angiotensin converting enzyme II (ACE2). SARS-CoV causes high fever in almost all patients, while SARS-CoV-2 does not. Moreover, analysis of the clinical data revealed that the higher body temperature is a protective factor in COVID-19 patients, making us to hypothesize a temperature-dependent binding affinity of SARS-CoV-2 to human ACE2 receptor. In this study, our molecular dynamics simulation and protein surface plasmon resonance cohesively proved the SARS-CoV-2-ACE2 binding was less affinitive and stable under 40 °C (~18 nM) than the optimum temperature 37 °C (6.2 nM), while SARS-CoV-ACE2 binding was not (6.4 nM vs. 8.5 nM), which evidenced the temperature-dependent affinity and explained that higher temperature is related to better clinical outcome. The decreased infection at higher temperature was also validated by pseudovirus entry assay using Vero and Caco-2 cells. We also demonstrated the structural basis of the distinct temperature-dependence of the two coronaviruses. Furthermore, the meta-analysis revealed a milder inflammatory response happened in the early stage of COVID-19, which explained the low fever tendency of COVID-19 and indicated the co-evolution of the viral protein structure and the inflammatory response. The temperature dependence of the binding affinity also indicated that higher body temperature at early stages might be beneficial to the COVID-19 patients.
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Affiliation(s)
- Zhonghua Zhou
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ziyi Yang
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Chi-Biotech Co. Ltd., Shenzhen 518023, China
| | - Junxian Ou
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Hong Zhang
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Chi-Biotech Co. Ltd., Shenzhen 518023, China
| | - Qiwei Zhang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong 510515, China
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, Guangdong 510632, China
| | - Ming Dong
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
- Chi-Biotech Co. Ltd., Shenzhen 518023, China
| | - Gong Zhang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
- Chi-Biotech Co. Ltd., Shenzhen 518023, China
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Oyewusi HA, Wahab RA, Huyop F. Dehalogenase-producing halophiles and their potential role in bioremediation. MARINE POLLUTION BULLETIN 2020; 160:111603. [PMID: 32919122 DOI: 10.1016/j.marpolbul.2020.111603] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/21/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
This review aims to briefly describe the potential role of dehalogenase-producing halophilic bacteria in decontamination of organohalide pollutants. Hypersaline habitats pose challenges to life because of low water activity (water content) and is considered as the largest and ultimate sink for pollutants due to naturally and anthropogenic activities in which a substantial amount of ecological contaminants are organohalides. Several such environments appear to host and support substantial diversity of extremely halophilic and halotolerant bacteria as well as halophilic archaea. Biodegradation of several toxic inorganic and organic compounds in both aerobic and anaerobic conditions are carried out by halophilic microbes. Therefore, remediation of polluted marine/hypersaline environments are the main scorching issues in the field of biotechnology. Although many microbial species are reported as effective pollutants degrader, but little has been isolated from marine/hypersaline environments. Therefore, more novel microbial species with dehalogenase-producing ability are still desired.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, PMB, 5351, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia; Enzyme Technology and Green Synthesis Group, Faculty of Science, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor, Malaysia.
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Taherimehr Z, Zaboli M, Torkzadeh-Mahani M. New insight into the molecular mechanism of the trehalose effect on urate oxidase stability. J Biomol Struct Dyn 2020; 40:1461-1471. [PMID: 33000700 DOI: 10.1080/07391102.2020.1828167] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Urate oxidase (EC 1.7.3.3) is a key enzyme in the purine metabolism which is applied in the treatment of gout and also, as a diagnostic reagent for uric acid detection. In the current study, the trehalose (TRE) effects as an additive on the structural stability and function of uricase were investigated. For recombinant expression of UOX in E. coli BL21 cells, firstly the coding sequence was subcloned into the pET-28a vector and after induction with IPTG, the recombinant UOX was purified by affinity chromatography using a Ni-NTA agarose column. To specify the trehalose effects on the urate oxidase (UOX) structure, optimum pH, optimum temperature, kinetic and thermodynamic parameters and also, the intrinsic fluorescence of UOX in the absence and presence of trehalose were examined. The UOX half-life is 24.32 min at 40 °C, whereas the UOX-TRE has a higher half-life (32.09 min) at this temperature. Generally, our findings confirm that trehalose has a protective effect on the enzyme structure. Optimum pH and temperature were 9 and 25 °C, respectively for both the naked and treated enzymes and their activity retained 42.18 and 64.80%, respectively after 48 h of incubation at room temperature. Also, theoretical results indicate that the random coil of the enzyme was converted to α-helix and β-sheet in the presence of trehalose which may preserve the integrity of the active site of the enzyme and increased the enzymatic activity. The MD simulation results indicated greater stability of the uricase structure in the presence of trehalose.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Taherimehr
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
| | - Maryam Zaboli
- Department of chemistry, Faculty of science, University of Birjand, Birjand, Iran
| | - Masoud Torkzadeh-Mahani
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman-Iran, Iran
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Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chem Sci 2020; 11:11162-11178. [PMID: 34094357 PMCID: PMC8162949 DOI: 10.1039/d0sc03367g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/10/2020] [Indexed: 12/01/2022] Open
Abstract
Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T m = 73.5 °C; ΔT m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.
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Affiliation(s)
- Klara Markova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Klaudia Chmelova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Sérgio M Marques
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Philippe Carpentier
- Université Grenoble Alpes, CNRS, CEA, Interdisciplinary Research Institute of Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM) 17 Avenue des Martyrs 38054 Grenoble France
- European Synchrotron Radiation Facility (ESRF) 71 Avenue des Martyrs 38043 Grenoble France
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University Kamenice 5 625 00 Brno Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno Pekarska 53 656 91 Brno Czech Republic
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Rana RM, Rampogu S, Abid NB, Zeb A, Parate S, Lee G, Yoon S, Kim Y, Kim D, Lee KW. In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics. Molecules 2020; 25:molecules25153510. [PMID: 32752079 PMCID: PMC7435474 DOI: 10.3390/molecules25153510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 11/16/2022] Open
Abstract
Drug resistance is a core issue in cancer chemotherapy. A known folate antagonist, methotrexate (MTX) inhibits human dihydrofolate reductase (hDHFR), the enzyme responsible for the catalysis of 7,8-dihydrofolate reduction to 5,6,7,8-tetrahydrofolate, in biosynthesis and cell proliferation. Structural change in the DHFR enzyme is a significant cause of resistance and the subsequent loss of MTX. In the current study, wild type hDHFR and double mutant (engineered variant) F31R/Q35E (PDB ID: 3EIG) were subject to computational study. Structure-based pharmacophore modeling was carried out for wild type (WT) and mutant (MT) (variant F31R/Q35E) hDHFR structures by generating ten models for each. Two pharmacophore models, WT-pharma and MT-pharma, were selected for further computations, and showed excellent ROC curve quality. Additionally, the selected pharmacophore models were validated by the Guner-Henry decoy test method, which yielded high goodness of fit for WT-hDHFR and MT-hDHFR. Using a SMILES string of MTX in ZINC15 with the selections of 'clean', in vitro and in vivo options, 32 MTX-analogs were obtained. Eight analogs were filtered out due to their drug-like properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment tests and Lipinski's Rule of five. WT-pharma and MT-pharma were further employed as a 3D query in virtual screening with drug-like MTX analogs. Subsequently, seven screening hits along with a reference compound (MTX) were subjected to molecular docking in the active site of WT- and MT-hDHFR. Through a clustering analysis and examination of protein-ligand interactions, one compound was found with a ChemPLP fitness score greater than that of MTX (reference compound). Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM/PBSA binding free energy. In conclusion, we report on an MTX analog which is capable of inhibiting hDHFR in wild type form, as well as in cases where the enzyme acquires resistance to drugs during chemotherapy treatment.
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Affiliation(s)
- Rabia Mukhtar Rana
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Noman Bin Abid
- Division of Life Science and Applied Life Science (BK 21), College of Natural Sciences, Gyeongsang National University, Jinju 52828, Korea;
| | - Amir Zeb
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Shraddha Parate
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Gihwan Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Sanghwa Yoon
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Yumi Kim
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Donghwan Kim
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (R.M.R.); (S.R.); (A.Z.); (S.P.); (G.L.); (S.Y.); (Y.K.); (D.K.)
- Correspondence: ; Tel.: +82-55-772-1360
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Pandey B, Aarthy M, Sharma M, Singh SK, Kumar V. Computational analysis identifies druggable mutations in human rBAT mediated Cystinuria. J Biomol Struct Dyn 2020; 39:5058-5067. [PMID: 32602810 DOI: 10.1080/07391102.2020.1784792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary distance between Cqm1 and rBAT, and rBAT ectodomain lacks the sequence motif which serves as binding-site for the BinAB toxin. Thus, BinAB toxin can be expected to remain safe for humans. rBAT (heavy subunit; SLC3A1) and catalytic b0,+AT (light subunit; SLC7A9), linked by single disulfide bond, mediate renal reabsorption of cystine and dibasic amino acids in Na+ independent manner. Mutations in rBAT cause type I Cystinuria disease which shows global prevalence, and rBAT can be thought as an important pharmacological target. However, 3D structures of rBAT and b0,+AT, the two components of b0,+ heteromeric amino acid transporter systems, are not available. We constructed a reliable homology model of rBAT using Cqm1 coordinates and that of transmembrane b0,+AT subunit using LAT1 coordinates. Mapping of pathogenic mutations onto rBAT ectodomain revealed their scattered distribution throughout the rBAT protein. Further, our computational simulations-based scoring of several known deleterious mutations of rBAT revealed that mutations those do not compromise the protein fold and stability, are localized on the same face of the molecule. These residues are expected to interact with the b0,+AT transporter. The present study thus identifies druggable sites on rBAT that could be targeted for the treatment of type I Cystinuria.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharati Pandey
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Murali Aarthy
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Mahima Sharma
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanjeev Kumar Singh
- Computer-aided drug design Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - Vinay Kumar
- Homi Bhabha National Institute, Mumbai, India
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Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Comput Struct Biotechnol J 2020; 18:1497-1508. [PMID: 32637047 PMCID: PMC7327271 DOI: 10.1016/j.csbj.2020.06.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (ΔT m up to 24 °C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts.
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Affiliation(s)
- Petra Babkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zuzana Dunajova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Martin Marek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, Bld. A13, 625 00 Brno, Czech Republic
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Antileishmanial activity evaluation of thiazolidine-2,4-dione against Leishmania infantum and Leishmania braziliensis. Parasitol Res 2020; 119:2263-2274. [PMID: 32462293 DOI: 10.1007/s00436-020-06706-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/05/2020] [Indexed: 01/04/2023]
Abstract
Leishmaniasis is responsible for approximately 65,000 annual deaths. Despite the mortality data, drugs available for the treatment of patients are insufficient and have moderate therapeutic efficacy in addition to serious adverse effects, which makes the development of new drugs urgent. To achieve this goal, the integration of kinetic and DSF assays against parasitic validated targets, along with phenotypic assays, can help the identification and optimization of bioactive compounds. Pteridine reductase 1 (PTR1), a validated target in Leishmania sp., is responsible for the reduction of folate and biopterin to tetrahydrofolate and tetrahydrobiopterin, respectively, both of which are essential for cell growth. In addition to the in vitro evaluation of 16 thiazolidine-2,4-dione derivatives against Leishmania major PTR1 (LmPTR1), using the differential scanning fluorimetry (ThermoFluor®), phenotypic assays were employed to evaluate the compound effect over Leishmania braziliensis (MHOM/BR/75/M2903) and Leishmania infantum (MHOM/BR/74/PP75) promastigotes viability. The ThermoFluor® results show that thiazolidine-2,4-dione derivatives have micromolar affinity to the target and equivalent activity on Leishmania cells. 2b is the most potent compound against L. infantum (EC50 = 23.45 ± 4.54 μM), whereas 2a is the most potent against L. braziliensis (EC50 = 44.16 ± 5.77 μM). This result suggests that lipophilic substituents on either-meta and/or-para positions of the benzylidene ring increase the potency against L. infantum. On the other hand, compound 2c (CE50 = 49.22 ± 7.71 μM) presented the highest selectivity index.
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Kumar R, Kumar R, Tanwar P, Rath GK, Kumar R, Kumar S, Dash N, Das P, Hussain S. Deciphering the impact of missense mutations on structure and dynamics of SMAD4 protein involved in pathogenesis of gall bladder cancer. J Biomol Struct Dyn 2020; 39:1940-1954. [PMID: 32151199 DOI: 10.1080/07391102.2020.1740789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gall bladder cancer (GBC) is the most common malignancy of biliary tract cancer associated with high mortality rate and poor prognosis due to lack of suitable biomarkers. In this study, we explored the structural and functional effects of different missense mutations occurs in SMAD4 that was associated with the development of GBC. We utilized in silico methods to predict the harmful effects of nonsynonymous missense mutations and monitored the stability of protein. We found that all mutations (D351N, G352E, R361C, R361H, E526Q) associated with SMAD4 were deleterious in nature resulting in the formation of deformed or unstable protein structure. Molecular dynamics simulation studies revealed how these mutations affect protein stability, structure, conformation and function. We observed, different mutants increase the compactness and rigidity of SMAD4 protein, alter secondary structure composition, decrease the surface area and protein-ligand interaction and affect its conformation. Findings of current work indicated that the analyzed mutations might affect the structure of protein and its caliber to interact with other molecules, which probably related to functional impairment of SMAD4 upon D351N, G352E, R361C, R361H, E526Q mutations and their involvement in cancer. Hence, the present study has significance of rational drug design and further increase our understanding of GBC development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rakesh Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Rahul Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Pranay Tanwar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - G K Rath
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ritesh Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Nihar Dash
- Department of Gastrointestinal Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Prasenjit Das
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Showket Hussain
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, Noida, India
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Meng Q, Capra N, Palacio CM, Lanfranchi E, Otzen M, van Schie LZ, Rozeboom HJ, Thunnissen AMWH, Wijma HJ, Janssen DB. Robust ω-Transaminases by Computational Stabilization of the Subunit Interface. ACS Catal 2020; 10:2915-2928. [PMID: 32953233 PMCID: PMC7493286 DOI: 10.1021/acscatal.9b05223] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/31/2020] [Indexed: 12/25/2022]
Abstract
Transaminases are attractive catalysts for the production of enantiopure amines. However, the poor stability of these enzymes often limits their application in biocatalysis. Here, we used a framework for enzyme stability engineering by computational library design (FRESCO) to stabilize the homodimeric PLP fold type I ω-transaminase from Pseudomonas jessenii. A large number of surface-located point mutations and mutations predicted to stabilize the subunit interface were examined. Experimental screening revealed that 10 surface mutations out of 172 tested were indeed stabilizing (6% success), whereas testing 34 interface mutations gave 19 hits (56% success). Both the extent of stabilization and the spatial distribution of stabilizing mutations showed that the subunit interface was critical for stability. After mutations were combined, 2 very stable variants with 4 and 6 mutations were obtained, which in comparison to wild type (T m app = 62 °C) displayed T m app values of 80 and 85 °C, respectively. These two variants were also 5-fold more active at their optimum temperatures and tolerated high concentrations of isopropylamine and cosolvents. This allowed conversion of 100 mM acetophenone to (S)-1-phenylethylamine (>99% enantiomeric excess) with high yield (92%, in comparison to 24% with the wild-type transaminase). Crystal structures mostly confirmed the expected structural changes and revealed that the most stabilizing mutation, I154V, featured a rarely described stabilization mechanism: namely, removal of steric strain. The results show that computational interface redesign can be a rapid and powerful strategy for transaminase stabilization.
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Affiliation(s)
- Qinglong Meng
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Nikolas Capra
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Cyntia M. Palacio
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Elisa Lanfranchi
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luc Z. van Schie
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Alemasov NA, Ivanisenko NV, Ivanisenko VA. Learning the changes of barnase mutants thermostability from structural fluctuations obtained using anisotropic network modeling. J Mol Graph Model 2020; 97:107572. [PMID: 32114079 DOI: 10.1016/j.jmgm.2020.107572] [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: 11/11/2019] [Revised: 01/29/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Abstract
In biotechnology applications, rational design of new proteins with improved physico-chemical properties includes a number of important tasks. One of the greatest practical and fundamental challenges is the design of highly thermostable protein enzymes that maintain catalytic activity at high temperatures. This problem may be solved by introducing mutations into the wild-type enzyme protein. In this work, to predict the impact of such mutations in barnase protein we applied the anisotropic network modeling approach, revealing atomic fluctuations in structural regions that are changed in mutants compared to the wild-type protein. A regression model was constructed based on these structural features that can allow one to predict the thermal stability of new barnase mutants. Moreover, the analysis of regression model provides a mechanistic explanation of how the structural features can contribute to the thermal stability of barnase mutants.
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Affiliation(s)
- Nikolay A Alemasov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia.
| | - Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia
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Zhang QF, Hu S, Zhao WR, Huang J, Mei JQ, Mei LH. Parallel Strategy Increases the Thermostability and Activity of Glutamate Decarboxylase. Molecules 2020; 25:molecules25030690. [PMID: 32041144 PMCID: PMC7037157 DOI: 10.3390/molecules25030690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 11/29/2022] Open
Abstract
Glutamate decarboxylase (GAD; EC 4.1.1.15) is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme that specifically catalyzes the decarboxylation of L-glutamic acid to produce γ-aminobutyric acid (GABA), which exhibits several well-known physiological functions. However, glutamate decarboxylase from different sources has the common problem of poor thermostability that affects its application in industry. In this study, a parallel strategy comprising sequential analysis and free energy calculation was applied to identify critical amino acid sites affecting thermostability of GAD and select proper mutation contributing to improve structure rigidity of the enzyme. Two mutant enzymes, D203E and S325A, with higher thermostability were obtained, and their semi-inactivation temperature (T5015) values were 2.3 °C and 1.4 °C higher than the corresponding value of the wild-type enzyme (WT), respectively. Moreover, the mutant, S325A, exhibited enhanced activity compared to the wild type, with a 1.67-fold increase. The parallel strategy presented in this work proved to be an efficient tool for the reinforcement of protein thermostability.
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Affiliation(s)
- Qing-Fei Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China;
| | - Sheng Hu
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
| | - Wei-Rui Zhao
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Jia-Qi Mei
- Hangzhou Zhongmei Huadong Pharmaceutical Co. Ltd., Hangzhou 31011, China;
| | - Le-He Mei
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
- Correspondence: ; Tel.: +86-571-879-531-61
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