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Ni D, Zhang S, Huang Z, Liu X, Xu W, Zhang W, Mu W. Multistrategy Engineering of an Inulosucrase to Enhance the Activity and Thermostability for Efficient Production of Microbial Inulin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18100-18109. [PMID: 39090787 DOI: 10.1021/acs.jafc.4c05224] [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: 08/04/2024]
Abstract
Inulin has found commercial applications in the pharmaceutical, nutraceutical, and food industries due to its beneficial health effects. The enzymatic biosynthesis of microbial inulin has garnered increasing attention. In this study, molecular modification was applied to Lactobacillus mulieris UMB7800 inulosucrase, an enzyme that specifically produces high-molecular weight inulin, to enhance its catalytic activity and thermostability. Among the 18 variable regions, R5 was identified as a crucial region significantly impacting enzymatic activity by replacing it with more conserved sequences. Site-directed mutagenesis combined with saturated mutagenesis revealed that the mutant A250 V increased activity by 68%. Additionally, after screening candidate mutants by rational design, four single-point mutants, S344D, H434P, E526D, and G531P, were shown to enhance thermostability. The final combinational mutant, M5, exhibited a 66% increase in activity and a 5-fold enhancement in half-life at 55 °C. These findings are significant for understanding the catalytic activity and thermostability of inulosucrase and are promising for the development of microbial inulin biosynthesis platforms.
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Affiliation(s)
- Dawei Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
- Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Shuqi Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoyong Liu
- Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Wei Xu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
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2
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Lakic B, Beh C, Sarkar S, Yap SL, Cardoso P, Valery C, Hung A, Jones NC, Hoffmann SV, Blanch EW, Dyett B, Conn CE. Cubosome lipid nanocarriers for delivery of ultra-short antimicrobial peptides. J Colloid Interface Sci 2024; 677:1080-1097. [PMID: 39137610 DOI: 10.1016/j.jcis.2024.07.232] [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: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/30/2024] [Indexed: 08/15/2024]
Abstract
HYPOTHESIS Although antimicrobial peptides (AMPs) are a promising class of new antibiotics, their inherent susceptibility to degradation requires nanocarrier-mediated delivery. While cubosome nanocarriers have been extensively studied for delivery of AMPs, we do not currently understand why cubosome encapsulation improves antimicrobial efficacy for some compounds but not others. This study therefore aims to investigate the link between the mechanism of action and permeation efficiency of the peptides, their encapsulation efficacy, and the antimicrobial activity of these systems. EXPERIMENTS Encapsulation and delivery of Indolicidin, and its ultra-short derivative, Priscilicidin, were investigated using SAXS, cryo-TEM and circular dichroism. Molecular dynamics simulations were used to understand the loading of these peptides within cubosomes. The antimicrobial efficacy was assessed against gram-negative (E. coli) and gram-positive (MRSA) bacteria. FINDINGS A high ionic strength solution was required to facilitate high loading of the cationic AMPs, with bilayer encapsulation driven by tryptophan and Fmoc moieties. Cubosome encapsulation did not improve the antimicrobial efficacy of the AMPs consistent with their high permeation, as explained by a recent 'diffusion to capture model'. This suggests that cubosome encapsulation may not be an effective strategy for all antimicrobial compounds, paving the way for improved selection of nanocarriers for AMPs, and other antimicrobial compounds.
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Affiliation(s)
- Biserka Lakic
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia
| | - Chia Beh
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia
| | - Sampa Sarkar
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia
| | - Sue-Lyn Yap
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia
| | - Priscila Cardoso
- School of Health and Biomedical Science, Translational Immunology and Nanotechnology Theme, NanoBioPharm Research Group, RMIT University, Bundoora, VIC, Australia
| | - Celine Valery
- School of Health and Biomedical Science, Translational Immunology and Nanotechnology Theme, NanoBioPharm Research Group, RMIT University, Bundoora, VIC, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark
| | | | - Ewan W Blanch
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia.
| | - Brendan Dyett
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia.
| | - Charlotte E Conn
- School of Science, STEM College, RMIT University, Victoria, 3001 Australia.
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3
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Mahase V, Sobitan A, Yao Q, Shi X, Qin H, Kidane D, Tang Q, Teng S. Impact of Missense Mutations on Spike Protein Stability and Binding Affinity in the Omicron Variant. Viruses 2024; 16:1150. [PMID: 39066312 PMCID: PMC11281596 DOI: 10.3390/v16071150] [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: 06/20/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The global effort to combat the COVID-19 pandemic faces ongoing uncertainty with the emergence of Variants of Concern featuring numerous mutations on the Spike (S) protein. In particular, the Omicron Variant is distinguished by 32 mutations, including 10 within its receptor-binding domain (RBD). These mutations significantly impact viral infectivity and the efficacy of vaccines and antibodies currently in use for therapeutic purposes. In our study, we employed structure-based computational saturation mutagenesis approaches to predict the effects of Omicron missense mutations on RBD stability and binding affinity, comparing them to the original Wuhan-Hu-1 strain. Our results predict that mutations such as G431W and P507W induce the most substantial destabilizations in the Wuhan-Hu-1-S/Omicron-S RBD. Notably, we postulate that mutations in the Omicron-S exhibit a higher percentage of enhancing binding affinity compared to Wuhan-S. We found that the mutations at residue positions G447, Y449, F456, F486, and S496 led to significant changes in binding affinity. In summary, our findings may shed light on the widespread prevalence of Omicron mutations in human populations. The Omicron mutations that potentially enhance their affinity for human receptors may facilitate increased viral binding and internalization in infected cells, thereby enhancing infectivity. This informs the development of new neutralizing antibodies capable of targeting Omicron's immune-evading mutations, potentially aiding in the ongoing battle against the COVID-19 pandemic.
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Affiliation(s)
| | - Adebiyi Sobitan
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Qiaobin Yao
- Department of Biology, Howard University, Washington, DC 20059, USA
| | - Xinghua Shi
- Department of Computer & Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Hong Qin
- Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, TN 37403, USA
| | - Dawit Kidane
- Department of Physiology and Biophysics, Howard University College of Medicine, Washington, DC 20059, USA
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC 20059, USA
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4
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Alvarado Obando M, Rey-Varela D, Cava F, Dörr T. Genetic interaction mapping reveals functional relationships between peptidoglycan endopeptidases and carboxypeptidases. PLoS Genet 2024; 20:e1011234. [PMID: 38598601 PMCID: PMC11034669 DOI: 10.1371/journal.pgen.1011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulators in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium identified hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote EP activation. Our data thus reveal a more complex role of DacA1 in maintaining PG homeostasis than previously assumed.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Diego Rey-Varela
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host-Microbe Interactions and Disease (CIHMID), Ithaca, New York, United States of America
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5
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El Hassab MA, El-Hafeez AAA, Almahli H, Elsayed ZM, Eldehna WM, Hassan GS, Abou-Seri SM. Phthalimide-tethered isatins as novel poly(ADP-ribose) polymerase inhibitors: Design, synthesis, biological evaluations, and molecular modeling investigations. Arch Pharm (Weinheim) 2024; 357:e2300599. [PMID: 38100160 DOI: 10.1002/ardp.202300599] [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: 10/14/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 03/03/2024]
Abstract
Humanity is currently facing various diseases with significant mortality rates, particularly those associated with malignancies. Numerous enzymes and proteins have been identified as highly promising targets for the treatment of cancer. The poly(ADP-ribose) polymerases (PARPs) family comprises 17 members which are essential in DNA damage repair, allowing the survival of cancer cells. Unlike other PARP family members, PARP-1 and, to a lesser extent, PARP-2 show more than 90% activity in response to DNA damage. PARP-1 levels were shown to be elevated in various tumor cells, including breast, lung, ovarian, and prostate cancer and melanomas. Accordingly, novel series of phthalimide-tethered isatins (6a-n, 10a-e, and 11a-e) were synthesized as potential PARP-1 inhibitors endowed with anticancer activity. All the synthesized molecules were assessed against PARP-1, where compounds 6f and 10d showed nanomolar activities with IC50 = 15.56 ± 2.85 and 13.65 ± 1.42 nM, respectively. Also, the assessment of the antiproliferative effects of the synthesized isatins was conducted on four cancer cell lines: leukemia (K-562), liver (HepG2), and breast (MCF-7 and HCC1937) cancers. Superiorly, compounds 6f and 10d demonstrated submicromolar IC50 values against breast cancer MCF-7 (IC50 = 0.92 ± 0.18 and 0.67 ± 0.12 µM, respectively) and HCC1937 (IC50 = 0.88 ± 0.52 and 0.53 ± 0.11 µM, respectively) cell lines. In addition, compounds 6f and 10d induced arrest in the G2/M phase of the cell cycle as compared to untreated cells. Finally, in silico studies, including docking and molecular dynamic simulations, were performed to justify the biological results.
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Affiliation(s)
- Mahmoud A El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), Ras Sudr, South Sinai, Egypt
| | - Amer Ali Abd El-Hafeez
- Cancer Biology Department, Pharmacology and Experimental Oncology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Zainab M Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Ghaneya S Hassan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, Badr University in Cairo (BUC), Badr City, Egypt
| | - Sahar M Abou-Seri
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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6
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Klaewkla M, Wangpaiboon K, Pichyangkura R, Charoenwongpaiboon T. Unraveling the role of flexible coil near calcium binding site of levansucrase on thermostability and product profile via proline substitution and molecular dynamics simulations. Proteins 2024; 92:170-178. [PMID: 37753539 DOI: 10.1002/prot.26592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Due to its bioactivity and versatile applications, levan has appeared as a promising biomaterial. Levansucrase is responsible for the conversion of sucrose into levan. With the goal of enhancing levan production, the strategy for enhancing the stability of levansucrase is being intensively studied. To make proteins more stable under high temperatures, proline, the most rigid residue, can be introduced into previously flexible regions. Herein, G249, D250, N251, and H252 on the flexible coil close to the calcium binding site of Bacillus licheniformis levansucrase were replaced with proline. Mutations at G249P greatly enhance both the enzyme's thermodynamic and kinetic stability, while those at H252P improve solely the enzyme's kinetic stability. GPC analysis revealed that G249P synthesize more levan, but H252P generate primarily oligosaccharides. Molecular dynamics simulations (MD) and MM/GBSA analysis revealed that G249P mutation increased not only the stability of levansucrase, but also affinity toward fructan.
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Affiliation(s)
| | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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7
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Xu SY, Zhou L, Xu Y, Hong HY, Dai C, Wang YJ, Zheng YG. Recent advances in structure-based enzyme engineering for functional reconstruction. Biotechnol Bioeng 2023; 120:3427-3445. [PMID: 37638646 DOI: 10.1002/bit.28540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/27/2023] [Accepted: 08/15/2023] [Indexed: 08/29/2023]
Abstract
Structural information can help engineer enzymes. Usually, specific amino acids in particular regions are targeted for functional reconstruction to enhance the catalytic performance, including activity, stereoselectivity, and thermostability. Appropriate selection of target sites is the key to structure-based design, which requires elucidation of the structure-function relationships. Here, we summarize the mutations of residues in different specific regions, including active center, access tunnels, and flexible loops, on fine-tuning the catalytic performance of enzymes, and discuss the effects of altering the local structural environment on the functions. In addition, we keep up with the recent progress of structure-based approaches for enzyme engineering, aiming to provide some guidance on how to take advantage of the structural information.
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Affiliation(s)
- Shen-Yuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ying Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Chen Dai
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, Zhejiang, People's Republic of China
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Nowak JS, Otzen DE. Helping proteins come in from the cold: 5 burning questions about cold-active enzymes. BBA ADVANCES 2023; 5:100104. [PMID: 38162634 PMCID: PMC10755280 DOI: 10.1016/j.bbadva.2023.100104] [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: 07/10/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.
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Affiliation(s)
- Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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9
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de Souza AS, Amorim VMDF, de Souza RF, Guzzo CR. Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility. J Biomol Struct Dyn 2023; 41:9326-9343. [PMID: 36345794 DOI: 10.1080/07391102.2022.2142296] [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: 04/01/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric spikeWT and SpikeBA.1 for 300 ns. Our results show that SpikeBA.1 has more conformational flexibility than SpikeWT. Our principal component analysis (PCA) allowed us to observe a broader spectrum of different conformations for SpikeBA.1, mainly at N-terminal domain (NTD) and receptor-binding domain (RBD). Such increased flexibility could contribute to decreased neutralizing antibody recognition of this variant. Our molecular dynamics data show that the RBDBA.1 easily visits an up-conformational state and the prevalent D614G mutation is pivotal to explain molecular dynamics results for this variant because to lost hydrogen bonding interactions between the residue pairs K854SC/D614SC, Y837MC/D614MC, K835SC/D614SC, T859SC/D614SC. In addition, SpikeBA.1 residues near the furin cleavage site are more flexible than in SpikeWT, probably due to P681H and D614G substitutions. Finally, dynamical cross-correlation matrix (DCCM) analysis reveals that D614G and P681H may allosterically affect the cleavage site S1/S2. Conversely, S2' site may be influenced by residues located between NTD and RBD of a neighboring protomer of the SpikeWT. Such communication may be lost in SpikeBA.1, explaining the changes of the cell tropism in the viral infection. In addition, the movements of the NTDWT and NTDBA.1 may modulate the RBD conformation through allosteric effects. Taken together, our results explain how the structural aspects may explain the observed gains in infectivity, immune system evasion and transmissibility of the Omicron variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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10
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Niu X, Zhao R, Yan S, Pang Z, Li H, Yang X, Wang K. Chiral Materials: Progress, Applications, and Prospects. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303059. [PMID: 37217989 DOI: 10.1002/smll.202303059] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/10/2023] [Indexed: 05/24/2023]
Abstract
Chirality is a universal phenomenon in molecular and biological systems, denoting an asymmetric configurational property where an object cannot be superimposed onto its mirror image by any kind of translation or rotation, which is ubiquitous on the scale from neutrinos to spiral galaxies. Chirality plays a very important role in the life system. Many biological molecules in the life body show chirality, such as the "codebook" of the earth's biological diversity-DNA, nucleic acid, etc. Intriguingly, living organisms hierarchically consist of homochiral building blocks, for example, l-amino acids and d-sugars with unknown reason. When molecules with chirality interact with these chiral factors, only one conformation favors the positive development of life, that is, the chiral host environment can only selectively interact with chiral molecules of one of the conformations. The differences in chiral interactions are often manifested by chiral recognition, mutual matching, and interactions with chiral molecules, which means that the stereoselectivity of chiral molecules can produce changes in pharmacodynamics and pathology. Here, the latest investigations are summarized including the construction and applications of chiral materials based on natural small molecules as chiral source, natural biomacromolecules as chiral sources, and the material synthesized by design as a chiral source.
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Affiliation(s)
- Xiaohui Niu
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
| | - Rui Zhao
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
| | - Simeng Yan
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
| | - Zengwei Pang
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
| | - Hongxia Li
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
| | - Xing Yang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, P. R. China
| | - Kunjie Wang
- College of Petrochemical Technology, Lanzhou University of Technology, Lanzhou, 730050, P. R. China
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11
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Ramón A, Esteves A, Villadóniga C, Chalar C, Castro-Sowinski S. A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies. Braz J Microbiol 2023; 54:2259-2287. [PMID: 37477802 PMCID: PMC10484896 DOI: 10.1007/s42770-023-01057-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Carolina Villadóniga
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Cora Chalar
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
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12
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Obando MA, Dörr T. Novel role for peptidoglycan carboxypeptidases in maintaining the balance between bacterial cell wall synthesis and degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548665. [PMID: 37503280 PMCID: PMC10369974 DOI: 10.1101/2023.07.12.548665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulation factors in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium was answered by hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote PG degradation. Our data thus reveal a key role of DacA1 in maintaining the balance between PG synthesis and degradation.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
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13
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Jia R, Tian S, Yang Z, Sadiq FA, Wang L, Lu S, Zhang G, Li J. Tuning Thermostability and Catalytic Efficiency of Aflatoxin-Degrading Enzyme by Error-prone PCR. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12610-4. [PMID: 37300712 DOI: 10.1007/s00253-023-12610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023]
Abstract
In our previous work, a recombinant aflatoxin-degrading enzyme derived from Myxococcus fulvus (MADE) was reported. However, the low thermal stability of the enzyme had limitations for its use in industrial applications. In this study, we obtained an improved variant of recombinant MADE (rMADE) with enhanced thermostability and catalytic activity using error-prone PCR. Firstly, we constructed a mutant library containing over 5000 individual mutants. Three mutants with T50 values higher than the wild-type rMADE by 16.5 °C (rMADE-1124), 6.5 °C (rMADE-1795), and 9.8 °C (rMADE-2848) were screened by a high-throughput screening method. Additionally, the catalytic activity of rMADE-1795 and rMADE-2848 was improved by 81.5% and 67.7%, respectively, compared to the wild-type. Moreover, structural analysis revealed that replacement of acidic amino acids with basic amino acids by a mutation (D114H) in rMADE-2848 increased the polar interactions with surrounding residues and resulted in a threefold increase in the t1/2 value of the enzyme and made it more thermaltolerate. KEY POINTS: • Mutant libraries construction of a new aflatoxins degrading enzyme by error-prone PCR. • D114H/N295D mutant improved enzyme activity and thermostability. • The first reported enhanced thermostability of aflatoxins degrading enzyme better for its application.
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Affiliation(s)
- Ru Jia
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China.
| | - Senmiao Tian
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Zhaofeng Yang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Faizan Ahmed Sadiq
- Fisheries and Food, Technology & Food Science Unit, Flanders Research Institute for Agriculture, 9090, Melle, Belgium
| | - Lan Wang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Simeng Lu
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Guohua Zhang
- School of Life Science, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
| | - Jianhui Li
- College of Animal Sciences, Shanxi Agriculture University, Taigu, 030801, China
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14
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Gupta A, Sahu N, Singh VK, Sinha RP. Evolutionary aspects of mutation in functional motif and post-translational modifications in SARS-CoV-2 3CLpro (Mpro): an in-silico study. JOURNAL OF PROTEINS AND PROTEOMICS 2023; 14:1-11. [PMID: 37361001 PMCID: PMC10099016 DOI: 10.1007/s42485-023-00105-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/20/2023] [Accepted: 03/30/2023] [Indexed: 06/28/2023]
Abstract
SARS CoV-2 is the virus that caused the COVID-19 pandemic. The main protease is one of the most prominent pharmacological targets for developing anti-COVID-19 therapeutic drugs (Mpro); SARS-CoV-2 replication is dependent on this component. SARS CoV-2's Mpro/cysteine protease is quite identical to SARS CoV-1's Mpro/cysteine protease. However, there is limited information on its structural and conformational properties. The present study aims to perform a complete in silico evaluation of Mpro protein's physicochemical properties. The motif prediction, post-translational modifications, effect of point mutation, and phylogenetic links were studied with other homologs to understand the molecular and evolutionary mechanisms of these proteins. The Mpro protein sequence was obtained in FASTA format from the RCSB Protein Data Bank. The structure of this protein was further characterized and analyzed using standard bioinformatics methods. According to Mpro's in-silico characterization, the protein is a basic, non-polar, and thermally stable globular protein. The outcomes of the phylogenetic and synteny study showed that the protein's functional domain amino acid sequence is substantially conserved. Furthermore, it has undergone many changes at the motif level over time from porcine epidemic diarrhoea virus to SARS-CoV 2, possibly to achieve various functions. Several post-translational modifications (PTMs) were also observed, and the possibilities of changes in Mpro protein exhibit additional orders of peptidase function regulation. During heatmap development, the effect of a point mutation on the Mpro protein was seen. This protein's structural characterization will aid in a better understanding of its function and mechanism of action. Supplementary Information The online version contains supplementary material available at 10.1007/s42485-023-00105-9.
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Affiliation(s)
- Amit Gupta
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Niharika Sahu
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Rajeshwar P. Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
- University Center for Research and Development (UCRD), Chandigarh University, Chandigarh, India
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15
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Li B, Sun Y, Zhu X, Qian S, Pu J, Guo Y, Wu H, Zhang L, Xin Y. Aggregation Interface and Rigid Spots Sustain the Stable Framework of a Thermophilic N-Demethylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5614-5629. [PMID: 37000489 DOI: 10.1021/acs.jafc.3c00877] [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: 06/19/2023]
Abstract
Enzymes from thermophilic microorganisms usually show high thermostability, which is of great potential in industrial application; to understand the structural logic of these enzymes is helpful for the construction of robust biocatalysts. In this study, based on the crystal structure of an N-demethylase─TrSOX─with outstanding thermostability from Thermomicrobium roseum, substitutions were introduced on the aggregation interface and rigid spots to reduce the aggregation ratio and the rigidity. Four substitutions on the aggregation interface─V162S, M308S, F170S, and V306S─considerably reduced the thermostability and slightly enhanced the catalytic efficiency. In addition, the thermostable framework was considerably disrupted in several multiple P → G substitutions in several local motifs (P129G/P134G, P237G/P259G, and P259G/P276G). These structural fluctuations were in good accordance with whole-structure or partial root-mean-square deviation, radius of gyration H-bonds, and solvent-accessible surface area values in molecular dynamics simulation. Furthermore, these key spots were introduced into an unstable homolog from Bacillus sp., resulting in a dramatical increase in the half-life at 60 °C from <10 to 1440 min. These results could help understand the natural stable framework of thermophilic enzymes, which could be references for the construction of robust enzymes in industrial applications.
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Affiliation(s)
- Bingjie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuqian Sun
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Xinyi Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Siyu Qian
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Jiayang Pu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yuwen Guo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Haobo Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Liang Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
| | - Yu Xin
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Research Center for Cereal Fermentation and Food Bio Manufacturing, Jiangnan University, Wuxi 214122, Jiangsu, P.R. China
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16
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Rao D, Huo R, Yan Z, Guo Z, Liu W, Lu M, Luo H, Tao X, Yang W, Su L, Chen S, Wang L, Wu J. Multiple approaches of loop region modification for thermostability improvement of 4,6-α-glucanotransferase from Limosilactobacillus fermentum NCC 3057. Int J Biol Macromol 2023; 233:123536. [PMID: 36740130 DOI: 10.1016/j.ijbiomac.2023.123536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
4,6-α-glucanotransferase (4,6-α-GT), as a member of the glycoside hydrolase 70 (GH70) family, converts starch/maltooligosaccharides into α,1-6 bond-containing α-glucan and possesses potential applications in food, medical and related industries but does not satisfy the high-temperature requirement due to its poor thermostability. In this study, a 4,6-α-GT (ΔGtfB) from Limosilactobacillus fermentum NCC 3057 was used as a model enzyme to improve its thermostability. The loops of ΔGtfB as the target region were optimized using directed evolution, sequence alignment, and computer-aided design. A total of 11 positive mutants were obtained and iteratively combined to obtain a combined mutant CM9, with high resistance to temperature (50 °C). The activity of mutant CM9 was 2.08-fold the activity of the wild type, accompanied by a 5 °C higher optimal temperature, a 5.76 °C higher melting point (Tm, 59.46 °C), and an 11.95-fold longer half-life time (t1/2). The results showed that most of the polar residues in the loop region of ΔGtfB are mutated into rigid proline residues. Molecular dynamics simulation demonstrated that the root mean square fluctuation of CM9 significantly decreased by "Breathing" movement reduction of the loop region. This study provides a new strategy for improving the thermostability of 4,6-α-GT through rational loop region modification.
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Affiliation(s)
- Deming Rao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Runtian Huo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhengfei Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhiyong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Mengwei Lu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Hui Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiumei Tao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Weikang Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lei Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
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17
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Chernov KG, Manoilov KY, Oliinyk OS, Shcherbakova DM, Verkhusha VV. Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore. Int J Mol Sci 2023; 24:6526. [PMID: 37047499 PMCID: PMC10095432 DOI: 10.3390/ijms24076526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.
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Affiliation(s)
| | - Kyrylo Yu. Manoilov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olena S. Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daria M. Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vladislav V. Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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18
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Lerma Romero JA, Meyners C, Rupp N, Hausch F, Kolmar H. A protein engineering approach toward understanding FKBP51 conformational dynamics and mechanisms of ligand binding. Protein Eng Des Sel 2023; 36:gzad014. [PMID: 37903068 DOI: 10.1093/protein/gzad014] [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: 09/05/2023] [Revised: 10/15/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023] Open
Abstract
Most proteins are flexible molecules that coexist in an ensemble of several conformations. Point mutations in the amino acid sequence of a protein can trigger structural changes that drive the protein population to a conformation distinct from the native state. Here, we report a protein engineering approach to better understand protein dynamics and ligand binding of the FK506-binding protein 51 (FKBP51), a prospective target for stress-related diseases, metabolic disorders, some types of cancers and chronic pain. By randomizing selected regions of its ligand-binding domain and sorting yeast display libraries expressing these variants, mutants with high affinity to conformation-specific FKBP51 selective ligands were identified. These improved mutants are valuable tools for the discovery of novel selective ligands that preferentially and specifically bind the FKBP51 active site in its open conformation state. Moreover, they will help us understand the conformational dynamics and ligand binding mechanics of the FKBP51 binding pocket.
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Affiliation(s)
- Jorge A Lerma Romero
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Christian Meyners
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Nicole Rupp
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Felix Hausch
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt 64287, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
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19
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Wei Z, Chen J, Xu L, Liu N, Yang J, Wang S. Improving the thermostability of GH49 dextranase AoDex by site-directed mutagenesis. AMB Express 2023; 13:7. [PMID: 36656394 PMCID: PMC9852402 DOI: 10.1186/s13568-023-01513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 01/08/2023] [Indexed: 01/20/2023] Open
Abstract
As an indispensable enzyme for the hydrolysis of dextran, dextranase has been widely used in the fields of food and medicine. It should be noted that the weak thermostability of dextranase has become a restricted factor for industrial applications. This study aims to improve the thermostability of dextranase AoDex in glycoside hydrolase (GH) family 49 that derived from Arthrobacter oxydans KQ11. Some mutants were predicted and constructed based on B-factor analysis, PoPMuSiC and HotMuSiC algorithms, and four mutants exhibited higher heat resistance. Compared with the wild-type, mutant S357P showed the best improved thermostability with a 5.4-fold increase of half-life at 60 °C, and a 2.1-fold increase of half-life at 65 °C. Furthermore, S357V displayed the most obvious increase in enzymatic activity and thermostability simultaneously. Structural modeling analysis indicated that the improved thermostability of mutants might be attributed to the introduction of proline and hydrophobic effects, which generated the rigid optimization of the structural conformation. These results illustrated that it was effective to improve the thermostability of dextranase AoDex by rational design and site-directed mutagenesis. The thermostable mutant of dextranase AoDex has potential application value, and it can also provide references for engineering other thermostable dextranases of the GH49 family.
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Affiliation(s)
- Zhen Wei
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Jinling Chen
- grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Linxiang Xu
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Nannan Liu
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Jie Yang
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
| | - Shujun Wang
- grid.443480.f0000 0004 1800 0658Jiangsu Key Laboratory of Marine Bioresources and Environment, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang, 222005 China ,grid.443480.f0000 0004 1800 0658School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, 222005 China
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20
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Öten AM, Atak E, Taktak Karaca B, Fırtına S, Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2124111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Ahmet Melih Öten
- Biology Education Center, Faculty of Science and Technology, Uppsala University, Uppsala, Sweden
| | - Evren Atak
- Bioinformatics and System Biology, Bioengineering Department, Gebze Technical University, Kocaeli, Turkey
| | - Banu Taktak Karaca
- Molecular Biology & Genetics Department, Faculty of Natural Science and Engineering, Atlas University, Istanbul, Turkey
| | - Sinem Fırtına
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
| | - Aslı Kutlu
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
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21
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Fang Y, Liu F, Shi Y, Yang T, Liang C, Xin Y, Gu Z, Shi G, Zhang L. Hotspots and Mechanisms of Action of the Thermostable Framework of a Microbial Thermolipase. ACS Synth Biol 2022; 11:3460-3470. [PMID: 36173803 DOI: 10.1021/acssynbio.2c00360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The lipase TrLipB from Thermomicrobium roseum is highly thermostable. However, its thermostable skeleton and mechanism of action should be investigated for industrial applications. Toward this, TrLipB was crystallized using the hanging-drop vapor diffusion method and subjected to X-ray diffraction at 2.0 Å resolution in this study. The rigid sites, such as the prolines on the relatively flexible loops on the enzyme surface, were scanned. Soft substitutions of these sites were designed using both molecular dynamics (MD) simulation and site-directed mutagenesis. The thermostability of several substitutions decreased markedly, while the catalytic efficiencies of the P9G, P127G, P194G, and P300G mutants reduced substantially; additionally, the thermostable framework of the double mutant, P194G/P300G, was considerably perturbed. However, the substitutions on the lid of the enzyme, including P49G and P48G, promoted the catalytic efficiency to approximately 150% and slightly enhanced the thermostability below 80 °C. In MD simulations, the P100G, P194G, P100G/P194G, P194G/P300G, and P100G/P194G/P300G mutants showed high B-factors and RMSD values, whereas the secondary structures, radius of gyration, H-bonds, and solvent accessible surface areas of these mutants were markedly affected. Our observations will assist in understanding the natural framework of a stable lipase, which might contribute to its industrial applications.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu 214122, P.R. China
| | - Chaojuan Liang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China.,Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu 214122, P.R. China
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22
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Kaczor PT, Michałowski MA, Mozrzymas JW. α 1 Proline 277 Residues Regulate GABA AR Gating through M2-M3 Loop Interaction in the Interface Region. ACS Chem Neurosci 2022; 13:3044-3056. [PMID: 36219829 PMCID: PMC9634794 DOI: 10.1021/acschemneuro.2c00401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Cys-loop receptors are a superfamily of transmembrane, pentameric receptors that play a crucial role in mammalian CNS signaling. Physiological activation of these receptors is typically initiated by neurotransmitter binding to the orthosteric binding site, located at the extracellular domain (ECD), which leads to the opening of the channel pore (gate) at the transmembrane domain (TMD). Whereas considerable knowledge on molecular mechanisms of Cys-loop receptor activation was gathered for the acetylcholine receptor, little is known with this respect about the GABAA receptor (GABAAR), which mediates cellular inhibition. Importantly, several static structures of GABAAR were recently described, paving the way to more in-depth molecular functional studies. Moreover, it has been pointed out that the TMD-ECD interface region plays a crucial role in transduction of conformational changes from the ligand binding site to the channel gate. One of the interface structures implicated in this transduction process is the M2-M3 loop with a highly conserved proline (P277) residue. To address this issue specifically for α1β2γ2L GABAAR, we choose to substitute proline α1P277 with amino acids with different physicochemical features such as electrostatic charge or their ability to change the loop flexibility. To address the functional impact of these mutations, we performed macroscopic and single-channel patch-clamp analyses together with modeling. Our findings revealed that mutation of α1P277 weakly affected agonist binding but was critical for all transitions of GABAAR gating: opening/closing, preactivation, and desensitization. In conclusion, we provide evidence that conservative α1P277 at the interface is strongly involved in regulating the receptor gating.
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23
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Chen L, Jiang K, Zhou Y, Zhu L, Chen X. Improving the Thermostability of α-Glucosidase from Xanthomonas campestris through Proline Substitutions Guided by Semi-rational Design. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Liu P, Guo J, Miao L, Liu H. Enhancing the secretion of a feruloyl esterase in Bacillus subtilis by signal peptide screening and rational design. Protein Expr Purif 2022; 200:106165. [PMID: 36038098 DOI: 10.1016/j.pep.2022.106165] [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] [Received: 07/08/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Feruloyl esterase is a subclass of α/β hydrolase, which could release ferulic acid from biomass residues for use as an efficient additive in food or pharmaceutical industries. In the present study, a feruloyl esterase with broad substrate specificity was characterised and secreted by Bacillus subtilis WB600. After codon usage optimisation and signal peptide library screening, the secretion amount of feruloyl esterase was enhanced by up to 10.2-fold in comparison with the base strain. The site-specific amino acid substitutions that facilitate protein folding further improved the secretion by about 1.5-fold. The purified rationally designed enzyme exhibited maximal activity against methyl ferulate at pH 6.5 and 65 °C. In the solid-state fermentation, the genetically engineered B. subtilis released about 37% of the total alkali-extractable ferulic acid in maize bran. This study provides a promising candidate for ferulic acid production and demonstrates that the secretion of a heterologous enzyme from B. subtilis can be cumulatively improved by changes in protein sequence features.
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Affiliation(s)
- Pulin Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jingxiao Guo
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Lihong Miao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Hanyan Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
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25
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Phenol sensing in nature is modulated via a conformational switch governed by dynamic allostery. J Biol Chem 2022; 298:102399. [PMID: 35988639 PMCID: PMC9556785 DOI: 10.1016/j.jbc.2022.102399] [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: 05/27/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
The NtrC family of proteins senses external stimuli and accordingly stimulates stress and virulence pathways via activation of associated σ54-dependent RNA polymerases. However, the structural determinants that mediate this activation are not well understood. Here, we establish using computational, structural, biochemical, and biophysical studies that MopR, an NtrC protein, harbors a dynamic bidirectional electrostatic network that connects the phenol pocket to two distal regions, namely the “G-hinge” and the “allosteric linker.” While the G-hinge influences the entry of phenol into the pocket, the allosteric linker passes the signal to the downstream ATPase domain. We show that phenol binding induces a rewiring of the electrostatic connections by eliciting dynamic allostery and demonstrates that perturbation of the core relay residues results in a complete loss of ATPase stimulation. Furthermore, we found a mutation of the G-hinge, ∼20 Å from the phenol pocket, promotes altered flexibility by shifting the pattern of conformational states accessed, leading to a protein with 7-fold enhanced phenol binding ability and enhanced transcriptional activation. Finally, we conducted a global analysis that illustrates that dynamic allostery-driven conserved community networks are universal and evolutionarily conserved across species. Taken together, these results provide insights into the mechanisms of dynamic allostery-mediated conformational changes in NtrC sensor proteins.
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26
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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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27
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Thermostability engineering of industrial enzymes through structure modification. Appl Microbiol Biotechnol 2022; 106:4845-4866. [PMID: 35804158 DOI: 10.1007/s00253-022-12067-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 07/02/2022] [Indexed: 01/14/2023]
Abstract
Thermostability is an essential requirement of enzymes in the industrial processes to catalyze the reactions at high temperatures; thus, enzyme engineering through directed evolution, semi-rational design and rational design are commonly employed to construct desired thermostable mutants. Several strategies are implemented to fulfill enzymes' thermostability demand including decreasing the entropy of the unfolded state through substitutions Gly → Xxx or Xxx → Pro, hydrogen bond, salt bridge, introducing two different simultaneous interactions through single mutant, hydrophobic interaction, filling the hydrophobic cavity core, decreasing surface hydrophobicity, truncating loop, aromatic-aromatic interaction and introducing positively charged residues to enzyme surface. In the current review, horizons about compatibility between secondary structures and substitutions at preferable structural positions to generate the most desirable thermostability in industrial enzymes are broadened. KEY POINTS: • Protein engineering is a powerful tool for generating thermostable industrial enzymes. • Directed evolution and rational design are practical approaches in enzyme engineering. • Substitutions in preferable structural positions can increase thermostability.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia. .,Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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28
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Manzer HS, Villarreal RI, Doran KS. Targeting the BspC-vimentin interaction to develop anti-virulence therapies during Group B streptococcal meningitis. PLoS Pathog 2022; 18:e1010397. [PMID: 35316308 PMCID: PMC8939794 DOI: 10.1371/journal.ppat.1010397] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 12/21/2022] Open
Abstract
Bacterial infections are a major cause of morbidity and mortality worldwide and the rise of antibiotic resistance necessitates development of alternative treatments. Pathogen adhesins that bind to host cells initiate disease pathogenesis and represent potential therapeutic targets. We have shown previously that the BspC adhesin in Group B Streptococcus (GBS), the leading cause of bacterial neonatal meningitis, interacts with host vimentin to promote attachment to brain endothelium and disease development. Here we determined that the BspC variable (V-) domain contains the vimentin binding site and promotes GBS adherence to brain endothelium. Site directed mutagenesis identified a binding pocket necessary for GBS host cell interaction and development of meningitis. Using a virtual structure-based drug screen we identified compounds that targeted the V-domain binding pocket, which blocked GBS adherence and entry into the brain in vivo. These data indicate the utility of targeting the pathogen-host interface to develop anti-virulence therapeutics.
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Affiliation(s)
- Haider S. Manzer
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
| | - Ricardo I. Villarreal
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
| | - Kelly S. Doran
- University of Colorado Anschutz Medical Campus, Department of Immunology and Microbiology, Aurora, Colorado, United States of America
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29
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Diamanti R, Srinivas V, Johansson A, Nordström A, Griese JJ, Lebrette H, Högbom M. Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase. FEBS Lett 2022; 596:1600-1610. [PMID: 35175627 PMCID: PMC9314684 DOI: 10.1002/1873-3468.14319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/11/2022]
Abstract
R2‐like ligand‐binding oxidase (R2lox) is a ferritin‐like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross‐link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry‐based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.
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Affiliation(s)
- Riccardo Diamanti
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
| | | | | | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden.,Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91, Stockholm, Sweden
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30
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Xin Y, Shen C, Tang M, Guo Z, Shi Y, Gu Z, Shao J, Zhang L. Recreating the natural evolutionary trend in key microdomains provides an effective strategy for engineering of a thermomicrobial N-demethylase. J Biol Chem 2022; 298:101656. [PMID: 35124004 PMCID: PMC8892156 DOI: 10.1016/j.jbc.2022.101656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 01/10/2023] Open
Abstract
N-demethylases have been reported to remove the methyl groups on primary or secondary amines, which could further affect the properties and functions of biomacromolecules or chemical compounds; however, the substrate scope and the robustness of N-demethylases have not been systematically investigated. Here we report the recreation of natural evolution in key microdomains of the Thermomicrobium roseum sarcosine oxidase (TrSOX), an N-demethylase with marked stability (melting temperature over 100 °C) and enantioselectivity, for enhanced substrate scope and catalytic efficiency on -C-N- bonds. We obtained the structure of TrSOX by crystallization and X-ray diffraction (XRD) for the initial framework. The natural evolution in the nonconserved residues of key microdomains—including the catalytic loop, coenzyme pocket, substrate pocket, and entrance site—was then identified using ancestral sequence reconstruction (ASR), and the substitutions that accrued during natural evolution were recreated by site-directed mutagenesis. The single and double substitution variants catalyzed the N-demethylation of N-methyl-L-amino acids up to 1800- and 6000-fold faster than the wild type, respectively. Additionally, these single substitution variants catalyzed the terminal N-demethylation of non-amino-acid compounds and the oxidation of the main chain -C-N- bond to a -C=N- bond in the nitrogen-containing heterocycle. Notably, these variants retained the enantioselectivity and stability of the initial framework. We conclude that the variants of TrSOX are of great potential use in N-methyl enantiomer resolution, main-chain Schiff base synthesis, and alkaloid modification or degradation.
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31
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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32
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Song Y, Cai H, Tan Z, Mussa N, Li ZJ. Mechanistic insights into inter-chain disulfide bond reduction of IgG1 and IgG4 antibodies. Appl Microbiol Biotechnol 2022; 106:1057-1066. [DOI: 10.1007/s00253-022-11778-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/24/2021] [Accepted: 01/13/2022] [Indexed: 11/29/2022]
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33
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Dietrich J, Lovell S, Veatch OJ, Butler MG. PHIP gene variants with protein modeling, interactions, and clinical phenotypes. Am J Med Genet A 2021; 188:579-589. [PMID: 34773373 DOI: 10.1002/ajmg.a.62557] [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: 07/30/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 01/24/2023]
Abstract
Variants in the pleckstrin homology domain-interacting protein (PHIP) gene are implicated in the clinical phenotype of Chung-Jansen syndrome, which includes dysmorphic features, cognitive dysfunction, aberrant behavior, and childhood onset obesity. Following a systematic literature review, 35 patients are reported to have unique PHIP variants impacting the encoded protein product. We summarize the status and frequency of these variants and relationship to clinical presentation. We also describe an additional patient with a rare, pathogenic variant due to a five base pair deletion leading to an altered codon at I307 but with a stop codon at 22 codons downstream; notably, a variant was identified at the same location as seen previously at protein position I307 in one other subject and a frameshift change at that protein position. We compare the clinical characteristics between the two patients and analyze whether certain types of gene defects impact clinical presentation in previously reported individuals. In addition, we predict structural protein models, which yielded unique differences between the wild-type and I307P-related mutant truncated proteins. Protein-protein interactions indicate involvement of POMC and related proteins with potential contribution to obesity, congenital, neuromuscular, and lipid disorders with heart, gastrointestinal, and rheumatoid diseases. With its surrounding proline-rich region, the I307P point mutation increases susceptibility to conformational rigidity and thermodynamic stability, ultimately impacting function as well as a stop codon downstream. Furthermore, the frameshift mutation seen in our patient may result in a truncated protein with a short abnormal region prior to the stop codon due to a five base pair deletion at I307 or target the protein for nonsense-mediated mRNA decay.
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Affiliation(s)
- Jordan Dietrich
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Scott Lovell
- Protein Structure Laboratory, University of Kansas, Lawrence, Kansas, USA
| | - Olivia J Veatch
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Merlin G Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas, USA
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34
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Gesteira TF, Marforio TD, Mueller JW, Calvaresi M, Coulson-Thomas VJ. Structural Determinants of Substrate Recognition and Catalysis by Heparan Sulfate Sulfotransferases. ACS Catal 2021; 11:10974-10987. [PMID: 37799563 PMCID: PMC10550706 DOI: 10.1021/acscatal.1c03088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Heparan sulfate (HS) and heparin contain imprinted "sulfation codes", which dictate their diverse physiological and pathological functions. A group of orchestrated biosynthetic enzymes cooperate in polymerizing and modifying HS chains. The biotechnological development of enzymes that can recreate this sulfation pattern on synthetic heparin is challenging, primarily due to the paucity of quantitative data for sulfotransferase enzymes. Herein, we identified critical structural characteristics that determine substrate specificity and shed light on the catalytic mechanism of sugar sulfation of two HS sulfotransferases, 2-O-sulfotransferase (HS2ST) and 6-O-sulfotransferase (HS6ST). Two sets of molecular clamps in HS2ST recognize appropriate substrates; these clamps flank the acceptor binding site on opposite sides. The hexuronic epimers, and not their puckers, have a critical influence on HS2ST selectivity. In contrast, HS6ST recognizes a broader range of substrates. This promiscuity is granted by a conserved tryptophan residue, W210, that positions the acceptor within the active site for catalysis by means of strong electrostatic interactions. Lysines K131 and K132 act in concert with a second tryptophan, W153, shedding water molecules from within the active site, thus providing HS6ST with a binding preference toward 2-O-sulfated substrates. QM/MM calculations provided valuable mechanistic insights into the catalytic process, identifying that the sulfation of both HS2ST and HS6ST follows a SN2-like mechanism. When they are taken together, our findings reveal the molecular basis of how these enzymes recognize different substrates and catalyze sugar sulfation, enabling the generation of enzymes that could create specific heparin epitopes.
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Affiliation(s)
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, U.K
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Bologna 40126, Italy
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35
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Haghdoust F, Molakarimi M, Mirshahi M, Sajedi RH. Engineering aequorin to improve thermostability through rigidifying flexible sites. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Crit Rev Food Sci Nutr 2021; 63:2057-2073. [PMID: 34445912 DOI: 10.1080/10408398.2021.1970508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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Li J, Jiang L, Cao X, Wu Y, Lu F, Liu F, Li Y, Liu Y. Improving the activity and stability of Bacillus clausii alkaline protease using directed evolution and molecular dynamics simulation. Enzyme Microb Technol 2021; 147:109787. [PMID: 33992409 DOI: 10.1016/j.enzmictec.2021.109787] [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: 11/09/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/06/2023]
Abstract
Detergent enzymes have been developed extensively as eco-friendly substitutes for the harmful chemicals in detergent. Among them, alkaline protease accounts for a large share of detergent enzyme sales. Thus, improving the specific activity of alkaline protease could play an important role in reducing the cost of detergent enzymes. In our study, alkaline protease from Bacillus clausii (PRO) was used to construct a mutant library through directed evolution using error-prone PCR, and a variant (G95P) with 9-fold enhancement in specific activity was obtained. After incubation at a pH of 11.0 for 70 h, G95P maintained 67 % of its maximal activity, which was 46 % more than wild-type PRO (WT), indicating that G95P has better alkaline stability than WT. The thermostability of G95P was also enhanced, as G95P achieved 17 % initial activity after incubation for 50 h at 60 °C, while WT lost its activity. The MD simulation results verified that variant G95P possessed improved stability of its Gly95-Gly100 loop region and Arg19-Asp265 salt bridge, leading to enhanced stability and catalytic efficiency. This work enhances the understanding of the structure-function relationship of PRO and provides an academic foundation for improving the enzymatic properties of PRO to satisfy industrial requirements using protein engineering.
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Affiliation(s)
- Jialin Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Luying Jiang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xue Cao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Yifan Wu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
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Zhang C, Ding Y. Probing the Relation Between Community Evolution in Dynamic Residue Interaction Networks and Xylanase Thermostability. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:686-696. [PMID: 31217124 DOI: 10.1109/tcbb.2019.2922906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Residue-residue interactions are the basis of protein thermostability. The molecular conformations of Streptomyces lividans xylanase (xyna_strli) and Thermoascus aurantiacus xylanase (xyna_theau) at 300K, 325K and 350K were obtained by Molecular Dynamics (MD) simulations. Dynamic weighted residue interaction networks were constructed and the rigid-communities were detected using the ESPRA algorithm and the Evolving Graph+Fast-Newman algorithm. The residues in the rigid-communities are primarily located in loop2, short helixes α2', α3', α4' and helixes α3 and α4. Thus, the rigid-community is close to the N-terminus of xylanase, which is usually stabilized to increase thermostability using site-directed mutagenesis. The evolution of the rigid-community with increasing temperature shows a stable synergistic interaction between loop2, α2', α3' and α4' in xyna_theau. In particular, the short helixes α2' and α3' form a "thermo helix" to promote thermostability. In addition, tight global interactions between loop2, α2', α3', α3, α4' and α4 of xyna_theau are identified, consisting mainly of hydrogen bonds, van der Waals forces and π-π stacking. These residue interactions are more resistant to high temperatures than those in xyna_strli. Robust residue interactions within these secondary structures are key factors influencing xyna_strli and xyna_theau thermostability. Analyzing the rigid-community can elucidate the cooperation of secondary structures, which cannot be discovered from sequence and 3D structure alone.
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Singh S, Biswas S, Srivastava A, Mishra Y, Chaturvedi TP. In silico characterization and structural modeling of a homeobox protein MSX1 from Homo sapiens. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2020.100497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Han X, Hofmann L, de la Fuente M, Alexander N, Palczewski K, Nieman MT. PAR4 activation involves extracellular loop 3 and transmembrane residue Thr153. Blood 2020; 136:2217-2228. [PMID: 32575122 PMCID: PMC7645988 DOI: 10.1182/blood.2019004634] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/24/2020] [Indexed: 12/17/2022] Open
Abstract
Protease-activated receptor 4 (PAR4) mediates sustained thrombin signaling in platelets and is required for a stable thrombus. PAR4 is activated by proteolysis of the N terminus to expose a tethered ligand. The structural basis for PAR4 activation and the location of its ligand binding site (LBS) are unknown. Using hydrogen/deuterium exchange (H/D exchange), computational modeling, and signaling studies, we determined the molecular mechanism for tethered ligand-mediated PAR4 activation. H/D exchange identified that the LBS is composed of transmembrane 3 (TM3) domain and TM7. Unbiased computational modeling further predicted an interaction between Gly48 from the tethered ligand and Thr153 from the LBS. Mutating Thr153 significantly decreased PAR4 signaling. H/D exchange and modeling also showed that extracellular loop 3 (ECL3) serves as a gatekeeper for the interaction between the tethered ligand and LBS. A naturally occurring sequence variant (P310L, rs2227376) and 2 experimental mutations (S311A and P312L) determined that the rigidity conferred by prolines in ECL3 are essential for PAR4 activation. Finally, we examined the role of the polymorphism at position 310 in venous thromboembolism (VTE) using the International Network Against Venous Thrombosis (INVENT) consortium multi-ancestry genome-wide association study (GWAS) meta-analysis. Individuals with the PAR4 Leu310 allele had a 15% reduction in relative risk for VTE (odds ratio, 0.85; 95% confidence interval, 0.77-0.94) compared with the Pro310 allele. These data are consistent with our H/D exchange, molecular modeling, and signaling studies. In conclusion, we have uncovered the structural basis for PAR4 activation and identified a previously unrecognized role for PAR4 in VTE.
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Affiliation(s)
- Xu Han
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | - Lukas Hofmann
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | | | - Nathan Alexander
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
| | | | - Marvin T Nieman
- Case Western Reserve University, School of Medicine, Cleveland, OH; and
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41
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Insight into the significant roles of the Trp372 and flexible loop in directing the catalytic direction and substrate specificity in AGE superfamily enzymes. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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42
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Saiada F, Gallardo RA, Shivaprasad HL, Corsiglia C, Van Santen VL. Intestinal Tropism of an Infectious Bronchitis Virus Isolate Not Explained by Spike Protein Binding Specificity. Avian Dis 2020; 64:23-35. [PMID: 32267122 DOI: 10.1637/0005-2086-64.1.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/17/2019] [Indexed: 11/05/2022]
Abstract
An infectious bronchitis virus (IBV) with an unusual enteric tropism (CalEnt) was isolated from a California broiler flock exhibiting runting-stunting syndrome. IBV was detected in the small intestine, but not in the respiratory tract or kidney. During virus isolation in embryos, it did not replicate in chorioallantoic membrane (CAM) but could be recovered from intestines. Its S1 protein showed 93% amino acid sequence identity to a California variant isolated in 1999 (Cal99). Intestinal lesions were reproduced following ocular/nasal inoculation of specific-pathogen-free chickens, but respiratory signs and lesions were also present. The virus was detected in both respiratory and intestinal tissues. To determine whether the novel tropism of IBV CalEnt was due to an increased ability of its S1 protein to bind to the intestinal epithelium, we compared the binding of soluble trimeric recombinant S1 proteins derived from CalEnt and Cal99 to chicken tissues. Contrary to expectations, the CalEnt S1 protein did not bind to small intestine and, unlike Cal99 S1, did not bind to the respiratory epithelium or CAM. Using only the CalEnt S1 N-terminal domain or including the S2 ectodomain (lacking membrane and cytoplasmic domains), which have been shown to improve ArkDPI S1 protein binding, did not lead to detectable binding at the standard protein concentration to any tissue tested. Our results indicate no/poor binding of the CalEnt spike protein to both respiratory and intestinal tissues and thus do not support better attachment to intestinal epithelial cells as a reason for CalEnt's extended tropism. These results might reflect shortcomings of the assay, including that it does not detect potential contributions of the S1 C-terminal domain to attachment. We used bioinformatic approaches to explore the possibility that the unique tropism of CalEnt might be a result of functions of the S protein in cell-entry steps subsequent to attachment. These analyses suggest that CalEnt's S2 coding region was acquired through a recombination event and encodes a unique amino acid sequence at the putative recognition site for the protease that activates the S protein for fusion. Thus, S2 activation by tissue-specific proteases might facilitate CalEnt entry into intestinal epithelial cells and compensate for poor binding by its S1 protein.
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Affiliation(s)
- Farjana Saiada
- Department of Pathobiology, 264 Greene Hall, College of Veterinary Medicine, Auburn University, Auburn, AL 36849
| | - Rodrigo A Gallardo
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616
| | - H L Shivaprasad
- University of California, California Animal Health and Food Safety Laboratory Tulare Branch, Tulare, CA 93274
| | | | - Vicky L Van Santen
- Department of Pathobiology, 264 Greene Hall, College of Veterinary Medicine, Auburn University, Auburn, AL 36849,
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Singh S, Kumar K, Nath P, Goyal A. Role of glycine 256 residue in improving the catalytic efficiency of mutant endoglucanase of family 5 glycoside hydrolase from Bacillus amyloliquefaciens SS35. Biotechnol Bioeng 2020; 117:2668-2682. [PMID: 32484905 DOI: 10.1002/bit.27448] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/24/2020] [Accepted: 05/31/2020] [Indexed: 11/07/2022]
Abstract
Wild-type, BaGH5-WT and mutant, BaGH5-UV2 (aspartate residue mutated to glycine), endoglucanases belonging to glycoside hydrolase family 5 (GH5), from wild-type, and UV2 mutant strain of Bacillus amyloliquefaciens SS35, respectively, were earlier cloned in pHTP0 cloning vector. In this study, genes encoding BaGH5-WT or BaGH5-UV2 were cloned into pET28a(+) expression-vector and expressed in Escherichia coli BL-21(DE3)pLysS cells. BaGH5-UV2 showed 10-fold (43.6 U/mg) higher specific activity against carboxymethylcellulose sodium salt (CMC-Na), higher optimal temperature by 10°C at 65°C, and 22-fold higher catalytic efficiency against CMC-Na, than BaGH5-WT. BaGH5-UV2 showed stability in wider acidic pH range (5.0-7.0) unlike BaGH5-WT in narrow basic pH range (7.0-7.5). BaGH5-UV2 displayed a mutation, Asp256Gly in L11 loop, connecting β6 -sheet with α6 -helix, near active site toward the domain surface of (α/β)8 -TIM barrel fold. Molecular dynamics simulation studies showed more stable structure, accessibility of substrate for a catalytic site, and increased flexibility of loop L11 of BaGH5-UV2 than the wild type, suggesting enhanced catalysis by BaGH5-UV2. Molecular docking analysis displayed enhanced hydrogen bond interactions of cello-oligosaccharides with BaGH5-UV2, unlike BaGH5-WT. Thus, Gly256 residue of loop L11 plays an important role in enhancing catalytic efficiency, and pH stability of GH5 endoglucanase. Therefore, these results help in protein engineering of GH5 endoglucanase for improved biochemical properties.
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Affiliation(s)
- Shweta Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.,DBT PAN-IIT Centre for Bioenergy, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Duru AD, Sun R, Allerbring EB, Chadderton J, Kadri N, Han X, Peqini K, Uchtenhagen H, Madhurantakam C, Pellegrino S, Sandalova T, Nygren PÅ, Turner SJ, Achour A. Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination. PLoS Pathog 2020; 16:e1008244. [PMID: 32365082 PMCID: PMC7224568 DOI: 10.1371/journal.ppat.1008244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/14/2020] [Accepted: 04/11/2020] [Indexed: 12/16/2022] Open
Abstract
Viral escape from CD8+ cytotoxic T lymphocyte responses correlates with disease progression and represents a significant challenge for vaccination. Here, we demonstrate that CD8+ T cell recognition of the naturally occurring MHC-I-restricted LCMV-associated immune escape variant Y4F is restored following vaccination with a proline-altered peptide ligand (APL). The APL increases MHC/peptide (pMHC) complex stability, rigidifies the peptide and facilitates T cell receptor (TCR) recognition through reduced entropy costs. Structural analyses of pMHC complexes before and after TCR binding, combined with biophysical analyses, revealed that although the TCR binds similarly to all complexes, the p3P modification alters the conformations of a very limited amount of specific MHC and peptide residues, facilitating efficient TCR recognition. This approach can be easily introduced in peptides restricted to other MHC alleles, and can be combined with currently available and future vaccination protocols in order to prevent viral immune escape.
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Affiliation(s)
- Adil Doganay Duru
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- NSU Cell Therapy Institute & Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Eva B. Allerbring
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jesseka Chadderton
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Nadir Kadri
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Kaliroi Peqini
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Hannes Uchtenhagen
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Chaithanya Madhurantakam
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI, School of Advanced Studies, New Delhi, India
| | - Sara Pellegrino
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Stephen J. Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- * E-mail:
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Gao X, Zhang X, Zhu N, Mou Y, Zhang H, Liu X, Wei P. Reshaping the substrate binding region of (R)-selective ω-transaminase for asymmetric synthesis of (R)-3-amino-1-butanol. Appl Microbiol Biotechnol 2020; 104:3959-3969. [PMID: 32185434 DOI: 10.1007/s00253-020-10539-6] [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] [Received: 01/11/2020] [Revised: 03/02/2020] [Accepted: 03/11/2020] [Indexed: 01/27/2023]
Abstract
(R)-Selective ω-transaminase (ω-TA) is a key enzyme for the asymmetric reductive amination of carbonyl compounds to produce chiral amines which are essential parts of many therapeutic compounds. However, its practical industrial applications are hindered by the low catalytic efficiency and poor thermostability of naturally occurring enzymes. In this work, we report the molecular modification of (R)-selective ω-TA from Aspergillus terreus (AtTA) to allow asymmetric reductive amination of 4-hydroxy-2-butanone, producing (R)-3-amino-1-butanol. Based on substrate docking analysis, 4 residues in the substrate tunnel and binding pocket of AtTA were selected as mutation hotspots. The screening procedure was facilitated by the construction of a "small-intelligent" library and the use of thin-layer chromatography for preliminary screening. The resulting mutant AtTA-M5 exhibited a 9.6-fold higher kcat/Km value and 9.4 °C higher [Formula: see text] than that of wild-type AtTA. Furthermore, the conversion of 20 and 50 g L-1 4-hydroxy-2-butanone by AtTA-M5 reached 90.8% and 79.1%, suggesting significant potential for production of (R)-3-amino-1-butanol. Under the same conditions, wild-type AtTA achieved less than 5% conversion. Moreover, the key mutation (S215P in AtTA) was validated in 7 other (R)-selective ω-TAs, indicating its general applicability in improving the catalytic efficiency of homologous (R)-selective ω-TAs.
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Affiliation(s)
- Xinxing Gao
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China.
| | - Xin Zhang
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China
| | - Nianqing Zhu
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China
| | - Yi Mou
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China
| | - Hailing Zhang
- Department of Biological Engineering, College of Life Science, Yantai University, Yantai, 264005, Shandong, China
| | - Xin Liu
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China
| | - Pinghe Wei
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, Taizhou, 225300, Jiangsu, China
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Shen W, Chen Y, Qiu S, Wang DN, Wang YJ, Zheng YG. Semi-rational engineering of a Kluyveromyces lactis aldo-keto reductase KlAKR for improved catalytic efficiency towards t-butyl 6-cyano-(3R, 5R)-dihydroxyhexanoate. Enzyme Microb Technol 2020; 132:109413. [DOI: 10.1016/j.enzmictec.2019.109413] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/13/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022]
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Tang H, Shi K, Shi C, Aihara H, Zhang J, Du G. Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy. J Biol Chem 2019; 294:18398-18407. [PMID: 31615894 PMCID: PMC6885650 DOI: 10.1074/jbc.ra119.010658] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/09/2019] [Indexed: 01/07/2023] Open
Abstract
Rational design-guided improvement of protein thermostability typically requires identification of residues or regions contributing to instability and introduction of mutations into these residues or regions. One popular method, B-FIT, utilizes B-factors to identify unstable residues or regions and combines them with other strategies, such as directed evolution. Here, we performed structure-based engineering to improve the thermostability of the subtilisin E-S7 (SES7) peptidase. The B-value of each residue was redefined in a normalized B-factor calculation, which was implemented with a refined bioinformatics analysis strategy to identify the critical area (loop 158-162) related to flexibility and to screen for suitable thermostable motif sequences in the Protein Data Bank that can act as transplant loops. In total, we analyzed 445 structures and identified 29 thermostable motifs as candidates. Using these motifs as a starting point, we performed iterative homologous modeling to obtain a desirable chimera loop and introduced five different mutations into this loop to construct thermostable SES7 proteins. Differential scanning fluorimetry revealed increases of 7.3 °C in the melting temperature of an SES7 variant designated M5 compared with the WT. The X-ray crystallographic structure of this variant was resolved at 1.96 Å resolution. The crystal structure disclosed that M5 forms more hydrogen bonds than the WT protein, consistent with design and molecular dynamics simulation results. In summary, the modified B-FIT strategy reported here has yielded a subtilisin variant with improved thermostability and promising industrial applications, supporting the notion that this modified method is a powerful tool for protein engineering.
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Affiliation(s)
- Heng Tang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455
| | - Cheng Shi
- School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, Minnesota 55455.
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
| | - Guocheng Du
- School of Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, Jiangsu, China.
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48
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Xu Z, Cen YK, Zou SP, Xue YP, Zheng YG. Recent advances in the improvement of enzyme thermostability by structure modification. Crit Rev Biotechnol 2019; 40:83-98. [DOI: 10.1080/07388551.2019.1682963] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zhe Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Ping Zou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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49
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Garcia Quiroz F, Li NK, Roberts S, Weber P, Dzuricky M, Weitzhandler I, Yingling YG, Chilkoti A. Intrinsically disordered proteins access a range of hysteretic phase separation behaviors. SCIENCE ADVANCES 2019; 5:eaax5177. [PMID: 31667345 PMCID: PMC6799979 DOI: 10.1126/sciadv.aax5177] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/26/2019] [Indexed: 05/13/2023]
Abstract
The phase separation behavior of intrinsically disordered proteins (IDPs) is thought of as analogous to that of polymers that undergo equilibrium lower or upper critical solution temperature (LCST and UCST, respectively) phase transition. This view, however, ignores possible nonequilibrium properties of protein assemblies. Here, by studying IDP polymers (IDPPs) composed of repeat motifs that encode LCST or UCST phase behavior, we discovered that IDPs can access a wide spectrum of nonequilibrium, hysteretic phase behaviors. Experimentally and through simulations, we show that hysteresis in IDPPs is tunable and that it emerges through increasingly stable interchain interactions in the insoluble phase. To explore the utility of hysteretic IDPPs, we engineer self-assembling nanostructures with tunable stability. These findings shine light on the rich phase separation behavior of IDPs and illustrate hysteresis as a design parameter to program nonequilibrium phase behavior in self-assembling materials.
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Affiliation(s)
| | - Nan K. Li
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Stefan Roberts
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Patrick Weber
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
| | - Michael Dzuricky
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Isaac Weitzhandler
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
- Corresponding author.
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50
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Pongpamorn P, Watthaisong P, Pimviriyakul P, Jaruwat A, Lawan N, Chitnumsub P, Chaiyen P. Identification of a Hotspot Residue for Improving the Thermostability of a Flavin‐Dependent Monooxygenase. Chembiochem 2019; 20:3020-3031. [DOI: 10.1002/cbic.201900413] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Pornkanok Pongpamorn
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Pratchaya Watthaisong
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Panu Pimviriyakul
- Department of BiotechnologyFaculty of Engineering and Industrial TechnologySilpakorn University 6 Rajamankha Nai Road Nakornpathom 73000 Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Narin Lawan
- Department of ChemistryFaculty of ScienceChiang Mai University Chiang Mai 50200 Thailand
| | - Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Paholyothin Road Klong 1 Klong Luang Pathumthani 12120 Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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