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S G SA, Rajasekaran R. Exploring Bacillus species xylanases for industrial applications: screening via thermostability and reaction modelling. J Mol Model 2024; 30:242. [PMID: 38955857 DOI: 10.1007/s00894-024-06048-2] [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: 04/29/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
CONTEXT Xylanases derived from Bacillus species hold significant importance in various large-scale production sectors, with increasing demand driven by biofuel production. However, despite their potential, the extreme environmental conditions often encountered in production settings have led to their underutilisation. To address this issue and enhance their efficacy under adverse conditions, we conducted a theoretical investigation on a group of five Bacillus species xylanases belonging to the glycoside hydrolase GH11 family. Bacillus sp. NCL 87-6-10 (sp_NCL 87-6-10) emerged as a potent candidate among the selected biocatalysts; this Bacillus strain exhibited high thermal stability and achieved a transition state with minimal energy requirements, thereby accelerating the biocatalytic reaction process. Our approach aims to provide support for experimentalists in the industrial sector, encouraging them to employ structural-based reaction modelling scrutinisation to predict the ability of targeted xylanases. METHODS Utilising crystal structure data available in the Carbohydrate-Active enzymes database, we aimed to analyse their structural capabilities in terms of thermal-stability and activity. Our investigation into identifying the most prominent Bacillus species xylanases unfolds with the help of the semi-empirical quantum mechanics MOPAC method integrated with the DRIVER program is used in calculations of reaction pathways to understand the activation energy. Additionally, we scrutinised the selected xylanases using various analyses, including constrained network analyses, intermolecular interactions of the enzyme-substrate complex and molecular orbital assessments calculated using the AM1 method with the MO-G model (MO-G AM1) to validate their reactivity.
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Affiliation(s)
- Sree Agash S G
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT Deemed to Be University), Vellore, Tamil Nadu, India
| | - R Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT Deemed to Be University), Vellore, Tamil Nadu, India.
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2
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Rizzuti B, Abian O, Velazquez-Campoy A, Neira JL. Conformational Stability of the N-Terminal Region of MDM2. Molecules 2023; 28:7578. [PMID: 38005300 PMCID: PMC10673428 DOI: 10.3390/molecules28227578] [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: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
MDM2 is an E3 ubiquitin ligase which is crucial for the degradation and inhibition of the key tumor-suppressor protein p53. In this work, we explored the stability and the conformational features of the N-terminal region of MDM2 (N-MDM2), through which it binds to the p53 protein as well as other protein partners. The isolated domain possessed a native-like conformational stability in a narrow pH range (7.0 to 10.0), as shown by intrinsic and 8-anilinonapthalene-1-sulfonic acid (ANS) fluorescence, far-UV circular dichroism (CD), and size exclusion chromatography (SEC). Guanidinium chloride (GdmCl) denaturation followed by intrinsic and ANS fluorescence, far-UV CD and SEC at physiological pH, and differential scanning calorimetry (DSC) and thermo-fluorescence experiments showed that (i) the conformational stability of isolated N-MDM2 was very low; and (ii) unfolding occurred through the presence of several intermediates. The presence of a hierarchy in the unfolding intermediates was also evidenced through DSC and by simulating the unfolding process with the help of computational techniques based on constraint network analysis (CNA). We propose that the low stability of this protein is related to its inherent flexibility and its ability to interact with several molecular partners through different routes.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
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3
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Sardiña-Peña AJ, Mesa-Ramos L, Iglesias-Figueroa BF, Ballinas-Casarrubias L, Siqueiros-Cendón TS, Espinoza-Sánchez EA, Flores-Holguín NR, Arévalo-Gallegos S, Rascón-Cruz Q. Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases' Thermostability. Int J Mol Sci 2023; 24:14513. [PMID: 37833959 PMCID: PMC10572972 DOI: 10.3390/ijms241914513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/10/2023] [Accepted: 09/10/2023] [Indexed: 10/15/2023] Open
Abstract
Due to their ability to produce isomaltulose, sucrose isomerases are enzymes that have caught the attention of researchers and entrepreneurs since the 1950s. However, their low activity and stability at temperatures above 40 °C have been a bottleneck for their industrial application. Specifically, the instability of these enzymes has been a challenge when it comes to their use for the synthesis and manufacturing of chemicals on a practical scale. This is because industrial processes often require biocatalysts that can withstand harsh reaction conditions, like high temperatures. Since the 1980s, there have been significant advancements in the thermal stabilization engineering of enzymes. Based on the literature from the past few decades and the latest achievements in protein engineering, this article systematically describes the strategies used to enhance the thermal stability of sucrose isomerases. Additionally, from a theoretical perspective, we discuss other potential mechanisms that could be used for this purpose.
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Affiliation(s)
- Amado Javier Sardiña-Peña
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Liber Mesa-Ramos
- Laboratorio de Microbiología III, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico;
| | - Blanca Flor Iglesias-Figueroa
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Lourdes Ballinas-Casarrubias
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Tania Samanta Siqueiros-Cendón
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Edward Alexander Espinoza-Sánchez
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Norma Rosario Flores-Holguín
- Laboratorio Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico;
| | - Sigifredo Arévalo-Gallegos
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
| | - Quintín Rascón-Cruz
- Laboratorio de Biotecnología I, Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitarios s/n Nuevo Campus Universitario, Chihuahua 31125, Mexico; (A.J.S.-P.); (B.F.I.-F.); (L.B.-C.); (T.S.S.-C.); (E.A.E.-S.); (S.A.-G.)
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4
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Liu L, Li J, Gai Y, Tian Z, Wang Y, Wang T, Liu P, Yuan Q, Ma H, Lee SY, Zhang D. Protein engineering and iterative multimodule optimization for vitamin B 6 production in Escherichia coli. Nat Commun 2023; 14:5304. [PMID: 37652926 PMCID: PMC10471632 DOI: 10.1038/s41467-023-40928-0] [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: 03/02/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.
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Affiliation(s)
- Linxia Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jinlong Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanming Gai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhizhong Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Yanyan Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tenghe Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Pi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 four program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- National Technology Innovation Center of Synthetic Biology, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Dotsenko A, Denisenko J, Zorov I, Wasserman L, Semenova M, Korolev A, Rozhkova A, Sinitsyn A. Single substitution in α-helix of active center enhanced thermostability of Aspergillus awamori exo-inulinase. J Mol Graph Model 2023; 119:108381. [PMID: 36473387 DOI: 10.1016/j.jmgm.2022.108381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Abstract
Exo-inulinases are applied in inulin hydrolysis and production of feed additives and need to be stable at temperatures of 60-95 °C. Aspergillus awamori exo-inulinase Inu1 is considerably thermostable, with a Tm of 73.2 °C. However, the thermostability of the enzyme should be improved. A single substitution G338A in α-helix in the active center of the enzyme provided a 3.5 °C improvement in Tm. The time of half-life at 70 °C and 80 °C was increased in 5.7- and 2.7-times, respectively, compared to wild-type. Molecular dynamics simulations demonstrated that the substitution G338A caused a decrease in RMSF not only for the α-helix 337-YAANI-341, but also for the catalytically active residues D41 and E241 and the amino acid residues forming the cleft of the active center. Calculations with Constraint Network Analysis for the variant G338A showed the increase in the stability of intramolecular clusters.
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Affiliation(s)
- Anna Dotsenko
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Jury Denisenko
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Ivan Zorov
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Luybov Wasserman
- Emanuel Institute of Biochemical Physics RAS, Moscow, 119334, Russia.
| | - Margarita Semenova
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
| | - Andrei Korolev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Aleksandra Rozhkova
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Arkady Sinitsyn
- FSI Federal Research Centre Fundamentals of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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6
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Marasco R, Fusi M, Coscolín C, Barozzi A, Almendral D, Bargiela R, Nutschel CGN, Pfleger C, Dittrich J, Gohlke H, Matesanz R, Sanchez-Carrillo S, Mapelli F, Chernikova TN, Golyshin PN, Ferrer M, Daffonchio D. Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes. Nat Commun 2023; 14:1045. [PMID: 36828822 PMCID: PMC9958047 DOI: 10.1038/s41467-023-36610-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/08/2023] [Indexed: 02/26/2023] Open
Abstract
Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme response in all cases. Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility confirms the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response.
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Affiliation(s)
- Ramona Marasco
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centre for Conservation and Restoration Science, Edinburgh Napier University Sighthill Campus, Edinburgh, UK
| | | | - Alan Barozzi
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | | | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jonas Dittrich
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC) and Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ruth Matesanz
- Spectroscopy Laboratory, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, Madrid, Spain
| | - Francesca Mapelli
- Department of Food Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Tatyana N Chernikova
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Deiniol Rd, Bangor, UK
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, Madrid, Spain.
| | - Daniele Daffonchio
- Biological and Environmental Sciences and Engineering Division (BESE), Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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7
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Functional, structural properties and interaction mechanism of soy protein isolate nanoparticles modified by high-performance protein-glutaminase. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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8
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Chandrasekhar G, Rajasekaran R. Theoretical investigations of TTR derived aggregation-prone peptides’ potential to biochemically attenuate the amyloidogenic propensities of V30 M TTR amyloid fibrils. J INDIAN CHEM SOC 2023. [DOI: 10.1016/j.jics.2023.100892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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9
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Rational Design of a Thermostable 2'-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites. Int J Mol Sci 2022; 23:ijms231911806. [PMID: 36233108 PMCID: PMC9570332 DOI: 10.3390/ijms231911806] [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: 08/03/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/24/2022] Open
Abstract
One of the major drawbacks of the industrial implementation of enzymatic processes is the low operational stability of the enzymes under tough industrial conditions. In this respect, the use of thermostable enzymes in the industry is gaining ground during the last decades. Herein, we report a structure-guided approach for the development of novel and thermostable 2′-deoxyribosyltransferases (NDTs) based on the computational design of disulfide bonds on hot spot positions. To this end, a small library of NDT variants from Lactobacillus delbrueckii (LdNDT) with introduced cysteine pairs was created. Among them, LdNDTS104C (100% retained activity) was chosen as the most thermostable variant, displaying a six- and two-fold enhanced long-term stability when stored at 55 °C (t1/255 °C ≈ 24 h) and 60 °C (t1/260 °C ≈ 4 h), respectively. Moreover, the biochemical characterization revealed that LdNDTS104C showed >60% relative activity across a broad range of temperature (30−90 °C) and pH (5−7). Finally, to study the potential application of LdNDTS104C as an industrial catalyst, the enzymatic synthesis of nelarabine was successfully carried out under different substrate conditions (1:1 and 3:1) at different reaction times. Under these experimental conditions, the production of nelarabine was increased up to 2.8-fold (72% conversion) compared with wild-type LdNDT.
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10
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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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11
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Heimsch KC, Gertzen CGW, Schuh AK, Nietzel T, Rahlfs S, Przyborski JM, Gohlke H, Schwarzländer M, Becker K, Fritz-Wolf K. Structure and Function of Redox-Sensitive Superfolder Green Fluorescent Protein Variant. Antioxid Redox Signal 2022; 37:1-18. [PMID: 35072524 PMCID: PMC9293687 DOI: 10.1089/ars.2021.0234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aims: Genetically encoded green fluorescent protein (GFP)-based redox biosensors are widely used to monitor specific and dynamic redox processes in living cells. Over the last few years, various biosensors for a variety of applications were engineered and enhanced to match the organism and cellular environments, which should be investigated. In this context, the unicellular intraerythrocytic parasite Plasmodium, the causative agent of malaria, represents a challenge, as the small size of the organism results in weak fluorescence signals that complicate precise measurements, especially for cell compartment-specific observations. To address this, we have functionally and structurally characterized an enhanced redox biosensor superfolder roGFP2 (sfroGFP2). Results: SfroGFP2 retains roGFP2-like behavior, yet with improved fluorescence intensity (FI) in cellulo. SfroGFP2-based redox biosensors are pH insensitive in a physiological pH range and show midpoint potentials comparable with roGFP2-based redox biosensors. Using crystallography and rigidity theory, we identified the superfolding mutations as being responsible for improved structural stability of the biosensor in a redox-sensitive environment, thus explaining the improved FI in cellulo. Innovation: This work provides insight into the structure and function of GFP-based redox biosensors. It describes an improved redox biosensor (sfroGFP2) suitable for measuring oxidizing effects within small cells where applicability of other redox sensor variants is limited. Conclusion: Improved structural stability of sfroGFP2 gives rise to increased FI in cellulo. Fusion to hGrx1 (human glutaredoxin-1) provides the hitherto most suitable biosensor for measuring oxidizing effects in Plasmodium. This sensor is of major interest for studying glutathione redox changes in small cells, as well as subcellular compartments in general. Antioxid. Redox Signal. 37, 1-18.
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Affiliation(s)
- Kim C Heimsch
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Katharina Schuh
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Thomas Nietzel
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Jude M Przyborski
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute of Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Karin Fritz-Wolf
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University Giessen, Giessen, Germany.,Max-Planck Institute of Medical Research, Heidelberg, Germany
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12
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Unusual commonality in active site structural features of substrate promiscuous and specialist enzymes. J Struct Biol 2022; 214:107835. [DOI: 10.1016/j.jsb.2022.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/26/2021] [Accepted: 01/23/2022] [Indexed: 11/21/2022]
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13
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Becker D, Bharatam PV, Gohlke H. F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. J Chem Inf Model 2021; 61:4023-4030. [PMID: 34370479 DOI: 10.1021/acs.jcim.1c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Of 57 human cytochrome P450 (CYP) enzymes, 12 metabolize 90% of xenobiotics. To our knowledge, no study has addressed the relation between enzyme dynamics and substrate promiscuity for more than three CYPs. Here, we show by constraint dilution simulations with the Constraint Network Analysis for the 12 isoforms that structural rigidity of the F/G region is significantly inversely correlated to the enzymes' substrate promiscuity. This highlights the functional importance of structural dynamics of the substrate tunnel.
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Affiliation(s)
- Daniel Becker
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, Sahibzada Ajit Singh Nagar, Mohali 160062, Punjab, India
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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14
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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15
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Pramanik S, Semenova MV, M Rozhkova A, Zorov IN, Korotkova O, Sinitsyn AP, Davari MD. An engineered cellobiohydrolase I for sustainable degradation of lignocellulosic biomass. Biotechnol Bioeng 2021; 118:4014-4027. [PMID: 34196389 DOI: 10.1002/bit.27877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/29/2021] [Accepted: 06/20/2021] [Indexed: 11/11/2022]
Abstract
This study provides computational-assisted engineering of the cellobiohydrolase I (CBH-I) from Penicillium verruculosum with simultaneous enhanced thermostability and tolerance in ionic liquids, deep eutectic solvent, and concentrated seawater without affecting its wild-type activity. Engineered triple variant CBH-I R1 (A65R-G415R-S181F) showed 2.48-fold higher thermostability in terms of relative activity at 65°C after 1 h of incubation when compared with CBH-I wild type. CBH-I R1 exhibited 1.87-fold, 1.36-fold, and 1.57-fold higher specific activities compared with CBH-I wild type in [Bmim]Cl (50 g/L), [Ch]Cl (50 g/L), and two-fold concentrated seawater, respectively. In the multicellulases mixture, CBH-I R1 showed higher hydrolytic efficiency to hydrolyze aspen wood compared with CBH-I wild type in the buffer, [Bmim]Cl (50 g/L), and two-fold concentrated seawater, respectively. Structural analysis revealed a molecular basis for the higher stability of the CBH-I structure in which A65R and G415R substitutions form salt bridges (D64 … R65, E411 … R415) and S181F forms π-π interaction (Y155 … F181), leading to stabilize surface-exposed flexible α-helixes and loop in the multidomain β-jelly roll fold structure, respectively. In conclusion, the variant CBH-I R1 could enable efficient lignocellulosic biomass degradation as a cost-effective alternative for the sustainable production of biofuels and value-added chemicals.
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Affiliation(s)
- Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Margarita V Semenova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Aleksandra M Rozhkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Ivan N Zorov
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Korotkova
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Arkady P Sinitsyn
- Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
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16
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Nutschel C, Coscolín C, David B, Mulnaes D, Ferrer M, Jaeger KE, Gohlke H. Promiscuous Esterases Counterintuitively Are Less Flexible than Specific Ones. J Chem Inf Model 2021; 61:2383-2395. [PMID: 33949194 DOI: 10.1021/acs.jcim.1c00152] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that an esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.
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Affiliation(s)
- Christina Nutschel
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Benoit David
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Daniel Mulnaes
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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17
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Bosch S, Sanchez-Freire E, del Pozo ML, C̆esnik M, Quesada J, Mate DM, Hernández K, Qi Y, Clapés P, Vasić-Rački Đ, Findrik Blažević Z, Berenguer J, Hidalgo A. Thermostability Engineering of a Class II Pyruvate Aldolase from Escherichia coli by in Vivo Folding Interference. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2021; 9:5430-5436. [PMID: 34589311 PMCID: PMC8461973 DOI: 10.1021/acssuschemeng.1c00699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/21/2021] [Indexed: 06/13/2023]
Abstract
The use of enzymes in industrial processes is often limited by the unavailability of biocatalysts with prolonged stability. Thermostable enzymes allow increased process temperature and thus higher substrate and product solubility, reuse of expensive biocatalysts, resistance against organic solvents, and better "evolvability" of enzymes. In this work, we have used an activity-independent method for the selection of thermostable variants of any protein in Thermus thermophilus through folding interference at high temperature of a thermostable antibiotic reporter protein at the C-terminus of a fusion protein. To generate a monomeric folding reporter, we have increased the thermostability of the moderately thermostable Hph5 variant of the hygromycin B phosphotransferase from Escherichia coli to meet the method requirements. The final Hph17 variant showed 1.5 °C higher melting temperature (T m) and 3-fold longer half-life at 65 °C compared to parental Hph5, with no changes in the steady-state kinetic parameters. Additionally, we demonstrate the validity of the reporter by stabilizing the 2-keto-3-deoxy-l-rhamnonate aldolase from E. coli (YfaU). The most thermostable multiple-mutated variants thus obtained, YfaU99 and YfaU103, showed increases of 2 and 2.9 °C in T m compared to the wild-type enzyme but severely lower retro-aldol activities (150- and 120-fold, respectively). After segregation of the mutations, the most thermostable single variant, Q107R, showed a T m 8.9 °C higher, a 16-fold improvement in half-life at 60 °C and higher operational stability than the wild-type, without substantial modification of the kinetic parameters.
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Affiliation(s)
- Sandra Bosch
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Esther Sanchez-Freire
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - María Luisa del Pozo
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Morana C̆esnik
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - Jaime Quesada
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Diana M. Mate
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Karel Hernández
- Institute
of Advanced Chemistry of Catalonia, Biotransformation and Bioactive
Molecules Group, Spanish National Research Council (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Yuyin Qi
- Prozomix
Ltd., Station Court, Haltwhistle, NE49 9HN Northumberland, United Kingdom
| | - Pere Clapés
- Institute
of Advanced Chemistry of Catalonia, Biotransformation and Bioactive
Molecules Group, Spanish National Research Council (IQAC−CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Đurđa Vasić-Rački
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - Zvjezdana Findrik Blažević
- University
of Zagreb, Faculty of Chemical
Engineering and Technology, Savska c. 16, HR-10000 Zagreb, Croatia
| | - José Berenguer
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Aurelio Hidalgo
- Department
of Molecular Biology, Center of Molecular Biology “Severo Ochoa”
(UAM-CSIC), Autonomous University of Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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18
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In Silico Therapeutic Peptide Design Against Pathogenic Domain Swapped Human Cystatin C Dimer. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10191-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Contreras F, Nutschel C, Beust L, Davari MD, Gohlke H, Schwaneberg U. Can constraint network analysis guide the identification phase of KnowVolution? A case study on improved thermostability of an endo-β-glucanase. Comput Struct Biotechnol J 2020; 19:743-751. [PMID: 33552446 PMCID: PMC7822948 DOI: 10.1016/j.csbj.2020.12.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulases are industrially important enzymes, e.g., in the production of bioethanol, in pulp and paper industry, feedstock, and textile. Thermostability is often a prerequisite for high process stability and improving thermostability without affecting specific activities at lower temperatures is challenging and often time-consuming. Protein engineering strategies that combine experimental and computational are emerging in order to reduce experimental screening efforts and speed up enzyme engineering campaigns. Constraint Network Analysis (CNA) is a promising computational method that identifies beneficial positions in enzymes to improve thermostability. In this study, we compare CNA and directed evolution in the identification of beneficial positions in order to evaluate the potential of CNA in protein engineering campaigns (e.g., in the identification phase of KnowVolution). We engineered the industrially relevant endoglucanase EGLII from Penicillium verruculosum towards increased thermostability. From the CNA approach, six variants were obtained with an up to 2-fold improvement in thermostability. The overall experimental burden was reduced to 40% utilizing the CNA method in comparison to directed evolution. On a variant level, the success rate was similar for both strategies, with 0.27% and 0.18% improved variants in the epPCR and CNA-guided library, respectively. In essence, CNA is an effective method for identification of positions that improve thermostability.
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Affiliation(s)
- Francisca Contreras
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Christina Nutschel
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Laura Beust
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
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20
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Ding D, Li J, Bai D, Fang H, Lin J, Zhang D. Biosensor-based monitoring of the central metabolic pathway metabolites. Biosens Bioelectron 2020; 167:112456. [DOI: 10.1016/j.bios.2020.112456] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/31/2022]
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21
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Cheng Z, Lan Y, Guo J, Ma D, Jiang S, Lai Q, Zhou Z, Peplowski L. Computational Design of Nitrile Hydratase from Pseudonocardia thermophila JCM3095 for Improved Thermostability. Molecules 2020; 25:molecules25204806. [PMID: 33086715 PMCID: PMC7587978 DOI: 10.3390/molecules25204806] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
High thermostability and catalytic activity are key properties for nitrile hydratase (NHase, EC 4.2.1.84) as a well-industrialized catalyst. In this study, rational design was applied to tailor the thermostability of NHase from Pseudonocardia thermophila JCM3095 (PtNHase) by combining FireProt server prediction and molecular dynamics (MD) simulation. Site-directed mutagenesis of non-catalytic residues provided by the rational design was subsequentially performed. The positive multiple-point mutant, namely, M10 (αI5P/αT18Y/αQ31L/αD92H/βA20P/βP38L/βF118W/βS130Y/βC189N/βC218V), was obtained and further analyzed. The Melting temperature (Tm) of the M10 mutant showed an increase by 3.2 °C and a substantial increase in residual activity of the enzyme at elevated temperatures was also observed. Moreover, the M10 mutant also showed a 2.1-fold increase in catalytic activity compared with the wild-type PtNHase. Molecular docking and MD simulations demonstrated better substrate affinity and improved thermostability for the mutant.
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Affiliation(s)
- Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Yao Lan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Dong Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Shijin Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Qianpeng Lai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao 226500, China
- Correspondence: (Z.Z.); (L.P.)
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Correspondence: (Z.Z.); (L.P.)
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22
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Nutschel C, Fulton A, Zimmermann O, Schwaneberg U, Jaeger KE, Gohlke H. Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. J Chem Inf Model 2020; 60:1568-1584. [PMID: 31905288 DOI: 10.1021/acs.jcim.9b00954] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Improving an enzyme's (thermo-)stability or tolerance against solvents and detergents is highly relevant in protein engineering and biotechnology. Recent developments have tended toward data-driven approaches, where available knowledge about the protein is used to identify substitution sites with high potential to yield protein variants with improved stability, and subsequently, substitutions are engineered by site-directed or site-saturation (SSM) mutagenesis. However, the development and validation of algorithms for data-driven approaches have been hampered by the lack of availability of large-scale data measured in a uniform way and being unbiased with respect to substitution types and locations. Here, we extend our knowledge on guidelines for protein engineering following a data-driven approach by scrutinizing the impact of substitution sites on thermostability or/and detergent tolerance for Bacillus subtilis lipase A (BsLipA) at very large scale. We systematically analyze a complete experimental SSM library of BsLipA containing all 3439 possible single variants, which was evaluated as to thermostability and tolerances against four detergents under respectively uniform conditions. Our results provide systematic and unbiased reference data at unprecedented scale for a biotechnologically important protein, identify consistently defined hot spot types for evaluating the performance of data-driven protein-engineering approaches, and show that the rigidity theory and ensemble-based approach Constraint Network Analysis yields hot spot predictions with an up to ninefold gain in precision over random classification.
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Affiliation(s)
- Christina Nutschel
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials, 52056 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52425 Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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23
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Critical effect of proline on thermostability of endoglucanase II from Penicillium verruculosum. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Astl L, Verkhivker GM. Data-driven computational analysis of allosteric proteins by exploring protein dynamics, residue coevolution and residue interaction networks. Biochim Biophys Acta Gen Subj 2019:S0304-4165(19)30179-5. [PMID: 31330173 DOI: 10.1016/j.bbagen.2019.07.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Computational studies of allosteric interactions have witnessed a recent renaissance fueled by the growing interest in modeling of the complex molecular assemblies and biological networks. Allosteric interactions in protein structures allow for molecular communication in signal transduction networks. METHODS In this work, we performed a large scale comprehensive and multi-faceted analysis of >300 diverse allosteric proteins and complexes with allosteric modulators. By modeling and exploring coarse-grained dynamics, residue coevolution, and residue interaction networks for allosteric proteins, we have determined unifying molecular signatures shared by allosteric systems. RESULTS The results of this study have suggested that allosteric inhibitors and allosteric activators may differentially affect global dynamics and network organization of protein systems, leading to diverse allosteric mechanisms. By using structural and functional data on protein kinases, we present a detailed case study that that included atomic-level analysis of coevolutionary networks in kinases bound with allosteric inhibitors and activators. CONCLUSIONS We have found that coevolutionary networks can form direct communication pathways connecting functional regions and can recapitulate key regulatory sites and interactions responsible for allosteric signaling in the studied protein systems. The results of this computational investigation are compared with the experimental studies and reveal molecular signatures of known regulatory hotspots in protein kinases. GENERAL SIGNIFICANCE This study has shown that allosteric inhibitors and allosteric activators can have a different effect on residue interaction networks and can exploit distinct regulatory mechanisms, which could open up opportunities for probing allostery and new drug combinations with broad range of activities.
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Affiliation(s)
- Lindy Astl
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America
| | - Gennady M Verkhivker
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, United States of America; Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States of America.
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25
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Agajanian S, Oluyemi O, Verkhivker GM. Integration of Random Forest Classifiers and Deep Convolutional Neural Networks for Classification and Biomolecular Modeling of Cancer Driver Mutations. Front Mol Biosci 2019; 6:44. [PMID: 31245384 PMCID: PMC6579812 DOI: 10.3389/fmolb.2019.00044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Development of machine learning solutions for prediction of functional and clinical significance of cancer driver genes and mutations are paramount in modern biomedical research and have gained a significant momentum in a recent decade. In this work, we integrate different machine learning approaches, including tree based methods, random forest and gradient boosted tree (GBT) classifiers along with deep convolutional neural networks (CNN) for prediction of cancer driver mutations in the genomic datasets. The feasibility of CNN in using raw nucleotide sequences for classification of cancer driver mutations was initially explored by employing label encoding, one hot encoding, and embedding to preprocess the DNA information. These classifiers were benchmarked against their tree-based alternatives in order to evaluate the performance on a relative scale. We then integrated DNA-based scores generated by CNN with various categories of conservational, evolutionary and functional features into a generalized random forest classifier. The results of this study have demonstrated that CNN can learn high level features from genomic information that are complementary to the ensemble-based predictors often employed for classification of cancer mutations. By combining deep learning-generated score with only two main ensemble-based functional features, we can achieve a superior performance of various machine learning classifiers. Our findings have also suggested that synergy of nucleotide-based deep learning scores and integrated metrics derived from protein sequence conservation scores can allow for robust classification of cancer driver mutations with a limited number of highly informative features. Machine learning predictions are leveraged in molecular simulations, protein stability, and network-based analysis of cancer mutations in the protein kinase genes to obtain insights about molecular signatures of driver mutations and enhance the interpretability of cancer-specific classification models.
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Affiliation(s)
- Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States.,Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
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26
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Muhammed MT, Son ÇD, İzgü F. Three dimensional structure prediction of panomycocin, a novel Exo-β-1,3-glucanase isolated from Wickerhamomyces anomalus NCYC 434 and the computational site-directed mutagenesis studies to enhance its thermal stability for therapeutic applications. Comput Biol Chem 2019; 80:270-277. [PMID: 31054539 DOI: 10.1016/j.compbiolchem.2019.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 10/26/2022]
Abstract
Panomycocin is a naturally produced potent antimycotic/antifungal protein secreted by the yeast Wickerhamomyces anomalus NCYC 434 with an exo-β-1,3-glucanase activity. In this study the three dimensional structure of panomycocin was predicted and the computational site-directed mutagenesis was performed to enhance its thermal stability in liquid formulations over the body temperature for topical therapeutic applications. Homology modeling was performed with MODELLER and I-TASSER. Among the generated models, the model with the lowest energy and DOPE score was selected for further loop modeling. The loop model was optimized and the reliability of the model was confirmed with ERRAT, Verify 3D and Ramachandran plot values. Enhancement of the thermal stability of the model was done using contemporary servers and programs such as SPDBViewer, CNA, I-Mutant2.0, Eris, AUTO-MUTE and MUpro. In the region outside the binding site of the model Leu52 Arg, Phe223Arg and Gly254Arg were found to be the best thermostabilizing mutations with 6.26 K, 6.26 K and 8.27 K increases, respectively. In the binding site Glu186Arg was found to be the best thermostabilizer mutation with a 9.58 K temperature increase. The results obtained in this study led us to design a mutant panomycocin that can be used as a novel antimycotic/antifungal drug in a liquid formulation for topical applications over the normal body temperature.
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Affiliation(s)
- Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta, Turkey
| | - Çağdaş Devrim Son
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey
| | - Fatih İzgü
- Department of Molecular Biology and Genetics, Middle East Technical University, Ankara, Turkey.
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27
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Astl L, Verkhivker GM. Atomistic Modeling of the ABL Kinase Regulation by Allosteric Modulators Using Structural Perturbation Analysis and Community-Based Network Reconstruction of Allosteric Communications. J Chem Theory Comput 2019; 15:3362-3380. [PMID: 31017783 DOI: 10.1021/acs.jctc.9b00119] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this work, we have examined the molecular mechanisms of allosteric regulation of the ABL tyrosine kinase at the atomic level. Atomistic modeling of the ABL complexes with a panel of allosteric modulators has been performed using a combination of molecular dynamics simulations, structural residue perturbation scanning, and a novel community analysis of the residue interaction networks. Our results have indicated that allosteric inhibitors and activators may exert a differential control on allosteric signaling between the kinase binding sites and functional regions. While the inhibitor binding can strengthen the closed ABL state and induce allosteric communications directed from the allosteric pocket to the ATP binding site, the DPH activator may induce a more dynamic open form and activate allosteric couplings between the ATP and substrate binding sites. By leveraging a network-centric theoretical framework, we have introduced a novel community analysis method and global topological parameters that have unveiled the hierarchical modularity and the intercommunity bridging sites in the residue interaction network. We have found that allosteric functional hotspots responsible for the kinase regulation may serve the intermodular bridges in the global interaction network. The central conclusion from this analysis is that the regulatory switch centers play a fundamental role in the modular network organization of ABL as the unique intercommunity bridges that connect the SH2 and SH3 domains with the catalytic core into a functional kinase assembly. The hierarchy of network organization in the ABL regulatory complexes may allow for the synergistic action of dense intercommunity links required for the robust signal transfer in the catalytic core and sparse network bridges acting as the regulatory control points that orchestrate allosteric transitions between the inhibited and active kinase forms.
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Affiliation(s)
- Lindy Astl
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology , Chapman University , One University Drive , Orange , California 92866 , United States
| | - Gennady M Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology , Chapman University , One University Drive , Orange , California 92866 , United States.,Department of Biomedical and Pharmaceutical Sciences , Chapman University School of Pharmacy , Irvine , California 92618 , United States
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28
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Bashirova A, Pramanik S, Volkov P, Rozhkova A, Nemashkalov V, Zorov I, Gusakov A, Sinitsyn A, Schwaneberg U, Davari MD. Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability. Int J Mol Sci 2019; 20:E1602. [PMID: 30935060 PMCID: PMC6479618 DOI: 10.3390/ijms20071602] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 01/29/2023] Open
Abstract
Endoglucanases (EGLs) are important components of multienzyme cocktails used in the production of a wide variety of fine and bulk chemicals from lignocellulosic feedstocks. However, a low thermostability and the loss of catalytic performance of EGLs at industrially required temperatures limit their commercial applications. A structure-based disulfide bond (DSB) engineering was carried out in order to improve the thermostability of EGLII from Penicillium verruculosum. Based on in silico prediction, two improved enzyme variants, S127C-A165C (DSB2) and Y171C-L201C (DSB3), were obtained. Both engineered enzymes displayed a 15⁻21% increase in specific activity against carboxymethylcellulose and β-glucan compared to the wild-type EGLII (EGLII-wt). After incubation at 70 °C for 2 h, they retained 52⁻58% of their activity, while EGLII-wt retained only 38% of its activity. At 80 °C, the enzyme-engineered forms retained 15⁻22% of their activity after 2 h, whereas EGLII-wt was completely inactivated after the same incubation time. Molecular dynamics simulations revealed that the introduced DSB rigidified a global structure of DSB2 and DSB3 variants, thus enhancing their thermostability. In conclusion, this work provides an insight into DSB protein engineering as a potential rational design strategy that might be applicable for improving the stability of other enzymes for industrial applications.
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Affiliation(s)
- Anna Bashirova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Subrata Pramanik
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
| | - Pavel Volkov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Aleksandra Rozhkova
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Vitaly Nemashkalov
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino 142292, Moscow region, Russia.
| | - Ivan Zorov
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Alexander Gusakov
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Arkady Sinitsyn
- Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences, Moscow 119071, Russia.
- Department of Chemistry, M.V.Lomonosov Moscow State University, Moscow 119991, Russia.
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
- DWI-Leibniz Institut für Interaktive Materialien, Forckenbeckstrasse 50, Aachen 52056, Germany.
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen 52074, Worringerweg 3, Germany.
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29
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Yonge F, Weixia X. Identification of Mitochondrial Proteins of Malaria Parasite Adding the New Parameter. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180608100348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Malaria has been one of the serious infectious diseases caused by Plasmodium falciparum (P. falciparum). Mitochondrial proteins of P. falciparum are regarded as effective drug targets against malaria. Thus, it is necessary to accurately identify mitochondrial proteins of malaria parasite. Many algorithms have been proposed for the prediction of mitochondrial proteins of malaria parasite and yielded the better results. However, the parameters used by these methods were primarily based on amino acid sequences. In this study, we added a novel parameter for predicting mitochondrial proteins of malaria parasite based on protein secondary structure. Firstly, we extracted three feature parameters, namely, three kinds of protein secondary structures compositions (3PSS), 20 amino acid compositions (20AAC) and 400 dipeptide compositions (400DC), and used the analysis of variance (ANOVA) to screen 400 dipeptides. Secondly, we adopted these features to predict mitochondrial proteins of malaria parasite by using support vector machine (SVM). Finally, we found that 1) adding the feature of protein secondary structure (3PSS) can indeed improve the prediction accuracy. This result demonstrated that the parameter of protein secondary structure is a valid feature in the prediction of mitochondrial proteins of malaria parasite; 2) feature combination can improve the prediction’s results; feature selection can reduce the dimension and simplify the calculation. We achieved the sensitivity (Sn) of 98.16%, the specificity (Sp) of 97.64% and overall accuracy (Acc) of 97.88% with 0.957 of Mathew’s correlation coefficient (MCC) by using 3PSS+ 20AAC+ 34DC as a feature in 15-fold cross-validation. This result is compared with that of the similar work in the same dataset, showing the superiority of our work.
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Affiliation(s)
- Feng Yonge
- College of Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Xie Weixia
- College of Science, Inner Mongolia Agriculture University, Hohhot 010018, China
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30
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Cantale C, Di Bianco D, Thiyagarajan K, Ammar K, Galeffi P. B genome specific polymorphism in the TdDRF1 gene is in relationship with grain yield. PLANTA 2018; 247:459-469. [PMID: 29075873 DOI: 10.1007/s00425-017-2799-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/17/2017] [Indexed: 06/07/2023]
Abstract
A and B genome copies of DRF1 gene in durum wheat were isolated and sequenced using gene variability. B genome specific polymorphism resulted, in a RIL population, in relationship with grain yield mainly in drought condition. Drought tolerance is one of the main components of yield potential and stability, and its improvement is a major challenge to breeders. Transcription factors are considered among the best candidate genes for developing functional markers, since they are components of the signal transduction pathways that coordinate the expression of several downstream genes. Polymorphisms of the Triticum durum dehydration responsive factor 1 (TdDRF1) gene that belongs to DREB2 transcription factor family were identified and specifically assigned to the A or B genome. A panel of primers was derived to selectively isolate the corresponding gene copies. These molecular information were also used to develop a new molecular marker: an allele-specific PCR assay discriminating two genotypes (Mohawk and Cocorit) was developed and used for screening a durum wheat recombinant inbred line population (RIL-pop) derived from the above genotypes. Phenotypic data from the RIL-pop grown during two seasons, under different environmental conditions, adopting an α-lattice design with two repetitions, were collected, analyzed and correlated with molecular data from the PCR assay. A significant association between a specific polymorphism in the B genome copy of the TdDRF1 gene and the grain yield in drought conditions were observed.
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Affiliation(s)
- Cristina Cantale
- ENEA, Casaccia Research Centre, Via Anguillarese 301, 00123, Rome, Italy
| | - Domenico Di Bianco
- ENEA, Casaccia Research Centre, Via Anguillarese 301, 00123, Rome, Italy
- SCUOLA SUPERIORE SANT'ANNA, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- CIMMYT (International Maize and Wheat Improvement Centre), Apartado Postal 6-641, 06600, Mexico D.F, Mexico
| | | | - Karim Ammar
- CIMMYT (International Maize and Wheat Improvement Centre), Apartado Postal 6-641, 06600, Mexico D.F, Mexico
| | - Patrizia Galeffi
- ENEA, Casaccia Research Centre, Via Anguillarese 301, 00123, Rome, Italy.
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Pandey V, Krishnan V, Basak N, Marathe A, Thimmegowda V, Dahuja A, Jolly M, Sachdev A. Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops. 3 Biotech 2018; 8:54. [PMID: 29354365 DOI: 10.1007/s13205-017-1053-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/17/2017] [Indexed: 02/06/2023] Open
Abstract
Designing low-phytate crops without affecting the developmental process in plants had led to the identification of ABCC5 gene in soybean. The GmABCC5 gene was identified and a partial gene sequence was cloned from popular Indian soybean genotype Pusa16. Conserved domains and motifs unique to ABC transporters were identified in the 30 homologous sequences retrieved by BLASTP analysis. The homologs were analyzed for their evolutionary relationship and physiochemical properties. Conserved domains, transmembrane architecture and secondary structure of GmABCC5 were predicted with the aid of computational tools. Analysis identified 53 alpha helices and 31 beta strands, predicting 60% residues in alpha conformation. A three-dimensional (3D) model for GmABCC5 was developed based on 5twv.1.B (Homo sapiens) template homology to gain better insight into its molecular mechanism of transport and sequestration. Spatio-temporal real-time PCR analysis identified mid-to-late seed developmental stages as the time window for the maximum GmABCC5 gene expression, a potential target stage for phytate reduction. Results of this study provide valuable insights into the structural and functional characteristics of GmABCC5, which may be further utilized for the development of nutritionally enriched low-phytate soybean with improved mineral bioavailability.
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Affiliation(s)
- Vanita Pandey
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, New Delhi 132 001 India
| | - Veda Krishnan
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Nabaneeta Basak
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, 753006 India
| | - Ashish Marathe
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vinutha Thimmegowda
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anil Dahuja
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Monica Jolly
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Archana Sachdev
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Czemeres J, Buse K, Verkhivker GM. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains. PLoS One 2017; 12:e0190267. [PMID: 29267381 PMCID: PMC5739471 DOI: 10.1371/journal.pone.0190267] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022] Open
Abstract
A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this mechanism may be exploited by the Hsp90-Cdc37 chaperone to recruit and protect intrinsically dynamic kinase clients from degradation. The results of this investigation are discussed and interpreted in the context of diverse experimental data, offering new insights into mechanisms of chaperone regulation and binding.
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Affiliation(s)
- Josh Czemeres
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Kurt Buse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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33
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Stetz G, Tse A, Verkhivker GM. Ensemble-based modeling and rigidity decomposition of allosteric interaction networks and communication pathways in cyclin-dependent kinases: Differentiating kinase clients of the Hsp90-Cdc37 chaperone. PLoS One 2017; 12:e0186089. [PMID: 29095844 PMCID: PMC5667858 DOI: 10.1371/journal.pone.0186089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
The overarching goal of delineating molecular principles underlying differentiation of protein kinase clients and chaperone-based modulation of kinase activity is fundamental to understanding activity of many oncogenic kinases that require chaperoning of Hsp70 and Hsp90 systems to attain a functionally competent active form. Despite structural similarities and common activation mechanisms shared by cyclin-dependent kinase (CDK) proteins, members of this family can exhibit vastly different chaperone preferences. The molecular determinants underlying chaperone dependencies of protein kinases are not fully understood as structurally similar kinases may often elicit distinct regulatory responses to the chaperone. The regulatory divergences observed for members of CDK family are of particular interest as functional diversification among these kinases may be related to variations in chaperone dependencies and can be exploited in drug discovery of personalized therapeutic agents. In this work, we report the results of a computational investigation of several members of CDK family (CDK5, CDK6, CDK9) that represented a broad repertoire of chaperone dependencies—from nonclient CDK5, to weak client CDK6, and strong client CDK9. By using molecular simulations of multiple crystal structures we characterized conformational ensembles and collective dynamics of CDK proteins. We found that the elevated dynamics of CDK9 can trigger imbalances in cooperative collective motions and reduce stability of the active fold, thus creating a cascade of favorable conditions for chaperone intervention. The ensemble-based modeling of residue interaction networks and community analysis determined how differences in modularity of allosteric networks and topography of communication pathways can be linked with the client status of CDK proteins. This analysis unveiled depleted modularity of the allosteric network in CDK9 that alters distribution of communication pathways and leads to impaired signaling in the client kinase. According to our results, these network features may uniquely define chaperone dependencies of CDK clients. The perturbation response scanning and rigidity decomposition approaches identified regulatory hotspots that mediate differences in stability and cooperativity of allosteric interaction networks in the CDK structures. By combining these synergistic approaches, our study revealed dynamic and network signatures that can differentiate kinase clients and rationalize subtle divergences in the activation mechanisms of CDK family members. The therapeutic implications of these results are illustrated by identifying structural hotspots of pathogenic mutations that preferentially target regions of the increased flexibility to enable modulation of activation changes. Our study offers a network-based perspective on dynamic kinase mechanisms and drug design by unravelling relationships between protein kinase dynamics, allosteric communications and chaperone dependencies.
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Affiliation(s)
- Gabrielle Stetz
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Amanda Tse
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- Department of Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, United States of America
- * E-mail:
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34
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Tossavainen H, Hellman M, Vainonen JP, Kangasjärvi J, Permi P. 1H, 13C and 15N NMR chemical shift assignments of A. thaliana RCD1 RST. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:207-210. [PMID: 28593560 DOI: 10.1007/s12104-017-9749-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
The A. thaliana RCD1 (radical-induced cell death1) protein is a cellular signaling hub protein which interacts with numerous plant transcription factors from different families. It consists of three conserved domains and intervening unstructured regions, the C-terminal RST domain being responsible for the interactions with the transcription factors. It has been shown that many partner proteins interact with RCD1 RST via their intrinsically disordered regions, and that the domain is able to house partners with divergent folds. We aim to structurally characterize the RCD1 RST domain and its complexes [complex with DREB2A]. Here we report the 1H, 15N and 13C chemical shift assignments of the backbone and sidechain atoms for RCD1 (468-589) containing the RST (510-567) domain.
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Affiliation(s)
- Helena Tossavainen
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maarit Hellman
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Julia P Vainonen
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Perttu Permi
- Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
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Graf M, Arenz S, Huter P, Dönhöfer A, Novácek J, Wilson DN. Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions. Nucleic Acids Res 2017; 45:2887-2896. [PMID: 27986857 PMCID: PMC5389730 DOI: 10.1093/nar/gkw1272] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/06/2016] [Indexed: 11/30/2022] Open
Abstract
Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.
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Affiliation(s)
- Michael Graf
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Stefan Arenz
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Paul Huter
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Alexandra Dönhöfer
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany
| | - Jirí Novácek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Daniel N Wilson
- Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, 81377 Munich, Germany.,Department of Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany
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Role of Cys73 in the thermostability of farnesyl diphosphate synthase from Geobacillus stearothermophilus. 3 Biotech 2017; 7:236. [PMID: 28695490 PMCID: PMC5503844 DOI: 10.1007/s13205-017-0792-8] [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: 05/13/2017] [Accepted: 06/14/2017] [Indexed: 11/04/2022] Open
Abstract
Farnesyl diphosphate synthase (FPPase) is an enzyme that catalyzes the condensation between one molecule of dimethylallyl diphosphate (DMAPP) and two molecules of isopentenyl diphosphate (IPP) to produce farnesyl diphosphate (FPP). FPP is an important precursor in the isoprenoid synthesis pathway. In this study, the crystal structure of FPPase from Geobacillus stearothermophilus (GsFPPase) was determined at 2.31 Å resolution. The structure of GsFPPase shows a three-layered all α-helical fold and conserved functional domains similar to other prenyltransferases. We have analyzed the structural features of GsFPPase related to thermostability and compared it with those of human and avian mesophilic FPPases. “Semi-conserved” regions which appear to be possible features contributing to the thermostability of FPPase were found.
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Fernández-Martín KG, Alvarez-Sánchez ME, Arana-Argáez VE, Alvarez-Sánchez LC, Lara-Riegos JC, Torres-Romero JC. Genome-wide identification, in silico characterization and expression analysis of ZIP-like genes from Trichomonas vaginalis in response to Zinc and Iron. Biometals 2017; 30:663-675. [PMID: 28733845 DOI: 10.1007/s10534-017-0034-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/12/2017] [Indexed: 01/29/2023]
Abstract
Trace elements such as Zinc and Iron are essential components of metalloproteins and serve as cofactors or structural elements for enzymes involved in several important biological processes in almost all organisms. Because either excess or insufficient levels of Zn and Fe can be harmful for the cells, the homeostatic levels of these trace minerals must be tightly regulated. The Zinc regulated transporter, Iron regulated transporter-like Proteins (ZIP) comprise a diverse family, with several paralogues in diverse organisms and are considered essential for the Zn and Fe uptake and homeostasis. Zn and Fe has been shown to regulate expression of proteins involved in metabolism and pathogenicity mechanisms in the protozoan pathogen Trichomonas vaginalis, in contrast high concentrations of these elements were also found to be toxic for T. vaginalis trophozoites. Nevertheless, Zn and Fe uptake and homeostasis mechanisms is not yet clear in this parasite. We performed a genome-wide analysis and localized the 8 members of the ZIP gene family in T. vaginalis (TvZIP1-8). The bioinformatic programs predicted that the TvZIP proteins are highly conserved and show similar properties to the reported in other ZIP orthologues. The expression patterns of TvZIP1, 3, 5 and 7 were diminished in presence of Zinc, while the rest of the TvZIP genes showed an unchanged profile in this condition. In addition, TvZIP2 and TvZIP4 showed a differential expression pattern in trophozoites growth under different Iron conditions. These results suggest that TvZIP genes encode membrane transporters that may be responsible for the Zn and Fe acquisition in T. vaginalis.
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Affiliation(s)
- K G Fernández-Martín
- Laboratorio de Bioquímica y Genética Molecular, Facultad de Química de la Universidad Autónoma de Yucatán, Calle 43 No. 613 x C. 90 Col. Inalámbrica, 97069, Mérida, Yucatán, Mexico
| | - M E Alvarez-Sánchez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), San Lorenzo # 290, Col. Del Valle, 03100, Ciudad de México, Mexico
| | - V E Arana-Argáez
- Laboratorio de Farmacología, Facultad de Química de la Universidad Autónoma de Yucatán, Calle 43 No. 613 x C. 90 Col. Inalámbrica, 97069, Mérida, Yucatán, Mexico
| | - L C Alvarez-Sánchez
- Laboratorio de Virología, Centro de Investigaciones Regionales "Dr, Hideyo Noguchi" de la Universidad Autónoma de Yucatán, Calle 43 s/n x C. 90 Col. Inalámbrica, 97069, Mérida, Yucatán, Mexico
| | - J C Lara-Riegos
- Laboratorio de Bioquímica y Genética Molecular, Facultad de Química de la Universidad Autónoma de Yucatán, Calle 43 No. 613 x C. 90 Col. Inalámbrica, 97069, Mérida, Yucatán, Mexico
| | - J C Torres-Romero
- Laboratorio de Bioquímica y Genética Molecular, Facultad de Química de la Universidad Autónoma de Yucatán, Calle 43 No. 613 x C. 90 Col. Inalámbrica, 97069, Mérida, Yucatán, Mexico.
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Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
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Hasumi H, Hasumi Y, Baba M, Nishi H, Furuya M, Vocke CD, Lang M, Irie N, Esumi C, Merino MJ, Kawahara T, Isono Y, Makiyama K, Warner AC, Haines DC, Wei MH, Zbar B, Hagenau H, Feigenbaum L, Kondo K, Nakaigawa N, Yao M, Metwalli AR, Marston Linehan W, Schmidt LS. H255Y and K508R missense mutations in tumour suppressor folliculin (FLCN) promote kidney cell proliferation. Hum Mol Genet 2017; 26:354-366. [PMID: 28007907 PMCID: PMC6075457 DOI: 10.1093/hmg/ddw392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/17/2016] [Accepted: 11/11/2016] [Indexed: 01/18/2023] Open
Abstract
Germline H255Y and K508R missense mutations in the folliculin (FLCN) gene have been identified in patients with bilateral multifocal (BMF) kidney tumours and clinical manifestations of Birt-Hogg-Dubé (BHD) syndrome, or with BMF kidney tumours as the only manifestation; however, their impact on FLCN function remains to be determined. In order to determine if FLCN H255Y and K508R missense mutations promote aberrant kidney cell proliferation leading to pathogenicity, we generated mouse models expressing these mutants using BAC recombineering technology and investigated their ability to rescue the multi-cystic phenotype of Flcn-deficient mouse kidneys. Flcn H255Y mutant transgene expression in kidney-targeted Flcn knockout mice did not rescue the multi-cystic kidney phenotype. However, expression of the Flcn K508R mutant transgene partially, but not completely, abrogated the phenotype. Notably, expression of the Flcn K508R mutant transgene in heterozygous Flcn knockout mice resulted in development of multi-cystic kidneys and cardiac hypertrophy in some mice. These results demonstrate that both FLCN H255Y and K508R missense mutations promote aberrant kidney cell proliferation, but to different degrees. Based on the phenotypes of our preclinical models, the FLCN H255Y mutant protein has lost it tumour suppressive function leading to the clinical manifestations of BHD, whereas the FLCN K508R mutant protein may have a dominant negative effect on the function of wild-type FLCN in regulating kidney cell proliferation and, therefore, act as an oncoprotein. These findings may provide mechanistic insight into the role of FLCN in regulating kidney cell proliferation and facilitate the development of novel therapeutics for FLCN-deficient kidney cancer.
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Affiliation(s)
- Hisashi Hasumi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | - Yukiko Hasumi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Masaya Baba
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hafumi Nishi
- Department of Applied Information Science, Tohoku University, Sendai, Japan
| | - Mitsuko Furuya
- Department of Molecular Pathology, Yokohama City University, Yokohama, Japan
| | - Cathy D. Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nobuko Irie
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Chiharu Esumi
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Maria J. Merino
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takashi Kawahara
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | - Yasuhiro Isono
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University, Yokohama, Japan
| | - Kazuhide Makiyama
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | | | | | - Ming-Hui Wei
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Berton Zbar
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Keiichi Kondo
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | - Noboru Nakaigawa
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | - Masahiro Yao
- Department of Urology and Molecular Genetics, Yokohama City University, Yokohama, Japan
| | - Adam R. Metwalli
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - W. Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura S. Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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Verkhivker GM. Network-based modelling and percolation analysis of conformational dynamics and activation in the CDK2 and CDK4 proteins: dynamic and energetic polarization of the kinase lobes may determine divergence of the regulatory mechanisms. MOLECULAR BIOSYSTEMS 2017; 13:2235-2253. [DOI: 10.1039/c7mb00355b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Network modeling and percolation analysis of conformational dynamics and energetics of regulatory mechanisms in cyclin-dependent kinases.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Biosciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Sci Rep 2016; 6:33213. [PMID: 27623708 PMCID: PMC5021933 DOI: 10.1038/srep33213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/12/2016] [Indexed: 01/23/2023] Open
Abstract
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.
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Affiliation(s)
- Alexander S. Fokas
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Daniel J. Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Sebastian E. Ahnert
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Alex W. Chin
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
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42
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Requirement of novel amino acid fragments of orphan nuclear receptor TR3/Nur77 for its functions in angiogenesis. Oncotarget 2016; 6:24261-76. [PMID: 26155943 PMCID: PMC4695184 DOI: 10.18632/oncotarget.4637] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/05/2015] [Indexed: 01/08/2023] Open
Abstract
Pathological angiogenesis is a hallmark of many diseases. We demonstrated that TR3/Nur77 is an excellent target for pro-angiogenesis and anti-angiogenesis therapies. Here, we report that TR3 transcriptionally regulates endothelial cell migration, permeability and the formation of actin stress fibers that is independent of RhoA GTPase. 1) Amino acid residues 344-GRR-346 and de-phosphorylation of amino acid residue serine 351 in the DNA binding domain, and 2) phosphorylation of amino acid residues in the 41-61 amino acid fragment of the transactivation domain, of TR3 are required for its induction of the formation of actin stress fibers, cell proliferation, migration and permeability. The 41-61 amino acid fragment contains one of the three potential protein interaction motifs in the transactivation domain of TR3, predicted by computational modeling and analysis. These studies further our understanding of the molecular mechanism, by which TR3 regulates angiogenesis, identify novel therapeutic targeted sites of TR3, and set the foundation for the development of high-throughput screening assays to identify compounds targeting TR3/Nur77 for pro-angiogenesis and anti-angiogenesis therapies.
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Rv2744c Is a PspA Ortholog That Regulates Lipid Droplet Homeostasis and Nonreplicating Persistence in Mycobacterium tuberculosis. J Bacteriol 2016; 198:1645-1661. [PMID: 27002134 DOI: 10.1128/jb.01001-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/16/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant cause of morbidity and mortality worldwide, despite the availability of a live attenuated vaccine and anti-TB antibiotics. The vast majority of individuals infected with M. tuberculosis develop an asymptomatic latent infection in which the bacterium survives within host-generated granulomatous lesions in a physiologically altered metabolic state of nonreplicating persistence. The granuloma represents an adverse environment, as M. tuberculosis is exposed to various stressors capable of disrupting the essential constituents of the bacterium. In Gram-negative and Gram-positive bacteria, resistance to cell envelope stressors that perturb the plasma membrane is mediated in part by proteins comprising the phage shock protein (Psp) system. PspA is an important component of the Psp system; in the presence of envelope stress, PspA localizes to the inner face of the plasma membrane, homo-oligomerizes to form a large scaffold-like complex, and helps maintain plasma membrane integrity to prevent a loss of proton motive force. M. tuberculosis and other members of the Mycobacterium genus are thought to encode a minimal functional unit of the Psp system, including an ortholog of PspA. Here, we show that Rv2744c possesses structural and physical characteristics that are consistent with its designation as a PspA family member. However, although Rv2744c is upregulated under conditions of cell envelope stress, loss of Rv2744c does not alter resistance to cell envelope stressors. Furthermore, Rv2744c localizes to the surface of lipid droplets in Mycobacterium spp. and regulates lipid droplet number, size, and M. tuberculosis persistence during anaerobically induced dormancy. Collectively, our results indicate that Rv2744c is a bona fide ortholog of PspA that may function in a novel role to regulate lipid droplet homeostasis and nonreplicating persistence (NRP) in M. tuberculosis IMPORTANCE Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease associated with significant morbidity and mortality worldwide. M. tuberculosis is capable of establishing lifelong asymptomatic infections in susceptible individuals and reactivating during periods of immune suppression to cause active disease. The determinants that are important for persistent infection of M. tuberculosis or for reactivation of this organism from latency are poorly understood. In this study, we describe our initial characterizations of Rv2744c, an ortholog of phage shock protein A (PspA) that regulates the homeostasis of lipid bodies and nonreplicating persistence in M. tuberculosis This function of PspA in M. tuberculosis is novel and suggests that PspA may represent a unique bacterial target upon which to base therapeutic interventions against this organism.
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Macalou S, Robey RW, Jabor Gozzi G, Shukla S, Grosjean I, Hegedus T, Ambudkar SV, Bates SE, Di Pietro A. The linker region of breast cancer resistance protein ABCG2 is critical for coupling of ATP-dependent drug transport. Cell Mol Life Sci 2016; 73:1927-37. [PMID: 26708291 PMCID: PMC7477947 DOI: 10.1007/s00018-015-2118-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/21/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
The ATP-binding cassette (ABC) transporters of class G display a different domain organisation than P-glycoprotein/ABCB1 and bacterial homologues with a nucleotide-binding domain preceding the transmembrane domain. The linker region connecting these domains is unique and its function and structure cannot be predicted. Sequence analysis revealed that the human ABCG2 linker contains a LSGGE sequence, homologous to the canonical C-motif/ABC signature present in all ABC nucleotide-binding domains. Predictions of disorder and of secondary structures indicated that this C2-sequence was highly mobile and located between an α-helix and a loop similarly to the C-motif. Point mutations of the two first residues of the C2-sequence fully abolished the transport-coupled ATPase activity, and led to the complete loss of cell resistance to mitoxantrone. The interaction with potent, selective and non-competitive, ABCG2 inhibitors was also significantly altered upon mutation. These results suggest an important mechanistic role for the C2-sequence of the ABCG2 linker region in ATP binding and/or hydrolysis coupled to drug efflux.
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Affiliation(s)
- S Macalou
- Equipe Labellisée Ligue 2014, BMSSI, UMR 5086 CNRS, Université Lyon 1, IBCP, 69007, Lyon, France
| | - R W Robey
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - G Jabor Gozzi
- Equipe Labellisée Ligue 2014, BMSSI, UMR 5086 CNRS, Université Lyon 1, IBCP, 69007, Lyon, France
| | - S Shukla
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - I Grosjean
- CelluloNet Biobank BB-0033-00072 Facility of UMS3444/US8/SFR Biosciences, IBCP, 69007, Lyon, France
| | - T Hegedus
- MTA-SE Molecular Biophysics Research Group, Hungarian Academy of Sciences and Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - S V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S E Bates
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - A Di Pietro
- Equipe Labellisée Ligue 2014, BMSSI, UMR 5086 CNRS, Université Lyon 1, IBCP, 69007, Lyon, France.
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Rathi PC, Fulton A, Jaeger KE, Gohlke H. Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis. PLoS Comput Biol 2016; 12:e1004754. [PMID: 27003415 PMCID: PMC4803202 DOI: 10.1371/journal.pcbi.1004754] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 01/14/2016] [Indexed: 11/29/2022] Open
Abstract
Protein thermostability is a crucial factor for biotechnological enzyme applications. Protein engineering studies aimed at improving thermostability have successfully applied both directed evolution and rational design. However, for rational approaches, the major challenge remains the prediction of mutation sites and optimal amino acid substitutions. Recently, we showed that such mutation sites can be identified as structural weak spots by rigidity theory-based thermal unfolding simulations of proteins. Here, we describe and validate a unique, ensemble-based, yet highly efficient strategy to predict optimal amino acid substitutions at structural weak spots for improving a protein’s thermostability. For this, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state has been found as the cause for thermostability. When applied prospectively to lipase A from Bacillus subtilis, we achieved both a high success rate (25% over all experimentally tested mutations, which raises to 60% if small-to-large residue mutations and mutations in the active site are excluded) in predicting significantly thermostabilized lipase variants and a remarkably large increase in those variants’ thermostability (up to 6.6°C) based on single amino acid mutations. When considering negative controls in addition and evaluating the performance of our approach as a binary classifier, the accuracy is 63% and increases to 83% if small-to-large residue mutations and mutations in the active site are excluded. The gain in precision (predictive value for increased thermostability) over random classification is 1.6-fold (2.4-fold). Furthermore, an increase in thermostability predicted by our approach significantly points to increased experimental thermostability (p < 0.05). These results suggest that our strategy is a valuable complement to existing methods for rational protein design aimed at improving thermostability. Protein thermostability is a crucial factor for biotechnological enzyme applications. However, performance studies of computational approaches for predicting effects of mutations on protein (thermo)stability have suggested that there is still room for improvement. We describe and validate a novel and unique strategy to predict optimal amino acid substitutions at structural weak spots. At variance with other rational approaches, we exploit the fact that in the majority of cases an increased structural rigidity of the folded state is the underlying cause for thermostability. When applied prospectively on lipase LipA from Bacillus subtilis, a high success rate in predicting thermostabilized lipase variants and a remarkably large increase in their thermostability is achieved. This demonstrates the value of the novel strategy, which extends the existing portfolio of methods for rational protein design.
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Affiliation(s)
- Prakash Chandra Rathi
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - Alexander Fulton
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University, Düsseldorf, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (KEJ); (HG)
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Department of Mathematics and Natural Sciences, Heinrich-Heine-University, Düsseldorf, Germany
- * E-mail: (KEJ); (HG)
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Meena RK, Shome S, Thakur S. Prediction of Phenotypic Effects of Variants Observed in LOC_Os04g36720 of FRO1 Gene in Rice (Oryza sativa L.). Interdiscip Sci 2016; 9:304-308. [PMID: 26885647 DOI: 10.1007/s12539-016-0152-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/11/2016] [Accepted: 02/03/2016] [Indexed: 12/01/2022]
Abstract
In rice, ferric-chelate reductase-1 (FRO1) (LOC_Os04g36720) gene was present on chromosome number 4 and its beginning and ending coordinates where coding sequence lies are 22182599 and 22186943, respectively. It plays a vital role in metal homeostasis and iron transportation in plants. Based on the alignment results, location of single-nucleotide variants is located in open reading frame and their effects of variants were predicted using SIFT sequence tool. The non-synonymous variants at position 342 and 436 lies in helical and coil parts of the protein, respectively, as predicted by Psi-pred server. PSI-Blast which resulted in significant hits and the most similar protein sequence (Accession ID: NP_001052896) with available sequence features displayed 100 % identity with query cover of 99 %. Results suggest the non-synonymous variant at position 436 (Accession ID: TBGI204002) lies in FAD-binding domain and nsSNV at position 342 (Accession ID: TBGI203998) lies in periphery of NADP. The SNPs were also analyzed for the deleterious effect by PANTHER subPSEC scores and I-mutant score, and it was postulated that SNPs would be hampering on biological as well as molecular function of FRO 1 gene of rice. A cutoff of -3 corresponds to a 50 % probability that a score is deleterious. From this, the probability that a given variant will cause a deleterious effect on protein function is estimated by P deleterious, such that a subPSEC score of -4 corresponds to a P deleterious of 0.79. Hence, to study the phenotypic consequences of variant TBGI204002, we performed comparative molecular docking studies of native modeled protein and protein with induced mutation as receptors and FAD as ligand to be utilized for binding. The docking process was performed by AutoDock 4.2 software with Lamarckian Genetic algorithm as computational algorithm. Results suggest binding energies are higher in case of mutation-induced protein which suggests presence of variant TBGI204002 enhances binding of FAD ligand at FAD-binding domain site. In case of TBGI203998, similar comparative docking procedure was performed with FAD as binding ligand, which suggests presence of variant does not impact FAD binding at the domain site. We revealed impact of SNPs on the protein structure and its function using sequence-based tools.
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Affiliation(s)
| | - Sayane Shome
- Aditya Biotech Lab and Research Pvt. Ltd., Raipur, Chhattisgarh, India
| | - Sanket Thakur
- Aditya Biotech Lab and Research Pvt. Ltd., Raipur, Chhattisgarh, India
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Savini F, Gallina L, Alberti A, Müller M, Scagliarini A. Bovine papillomavirus type 7 in Italy: complete genomes and sequence variants. Virus Genes 2016; 52:253-60. [PMID: 26837892 DOI: 10.1007/s11262-016-1298-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/19/2016] [Indexed: 01/09/2023]
Abstract
Two novel bovine papillomavirus type 7 (BPV-7) variants have been identified in teat cutaneous papillomas affecting dairy cows in northern Italy. The entire genome sequences of two BPV-7 Italian variants showed major sequence differences in the long control region (LCR) and in the L2 gene compared to the Japanese reference strain. In order to define the stability of these genetic variants, the L2 and LCR sequences of seven further BPV-7 positive isolates were characterized. An insertion of six amino acids in the L2 structural protein has been detected in all samples while different genetic variants have been identified for the LCR. These findings provide new insights on intra-type variability of BPVs and represent a starting point for future studies aimed at establishing the biological role of the different BPV genomic regions and investigating the pathogenic potential of papillomavirus variants.
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Affiliation(s)
- Federica Savini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Laura Gallina
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Alberto Alberti
- Dipartimento di Medicina Veterinaria, Università degli Studi di Sassari, Via Vienna 2, 07100, Sassari, Italy
| | - Martin Müller
- Infections and Cancer Program, German Cancer Research Center (DKFZ), F035, Im Neuenheimer Feld 242, 69120, Heidelberg, Germany
| | - Alessandra Scagliarini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
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Molecular Cloning, Expression Analysis, and Functional Characterization of the H(+)-Pyrophosphatase from Jatropha curcas. Appl Biochem Biotechnol 2015; 178:1273-85. [PMID: 26643082 DOI: 10.1007/s12010-015-1944-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
H(+)-pyrophosphatase (H(+)-PPase) is a primary pyrophosphate (PPi)-energized proton pump to generate electrochemical H(+) gradient for ATP production and substance translocations across membranes. It plays an important role in stress adaptation that was intensively substantiated by numerous transgenic plants overexpressing H(+)-PPases yet devoid of any correlated studies pointing to the elite energy plant, Jatropha curcas. Herein, we cloned the full length of J. curcas H(+)-PPase (JcVP1) complementary DNA (cDNA) by reverse transcription PCR, based on the assembled sequence of its ESTs highly matched to Hevea brasiliensis H(+)-PPase. This gene encodes a polypeptide of 765 amino acids that was predicted as a K(+)-dependent H(+)-PPase evolutionarily closest to those of other Euphorbiaceae plants. Many cis-regulatory elements relevant to environmental stresses, molecular signals, or tissue-specificity were identified by promoter prediction within the 1.5-kb region upstream of JcVP1 coding sequence. Meanwhile, the responses of JcVP1 expression to several common abiotic stresses (salt, drought, heat, cold) were characterized with a considerable accordance with the inherent stress tolerance of J. curcas. Moreover, we found that the heterologous expression of JcVP1 could significantly improve the salt tolerance in both recombinant Escherichia coli and Saccharomyces cerevisiae, and this effect could be further fortified in yeast by N-terminal addition of a vacuole-targeting signal peptide from the H(+)-PPase of Trypanosoma cruzi.
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Abstract
Gene-activating lipophilic compounds are carried into the nucleus when loaded on fatty-acid-binding proteins (FABP). Some of these proteins are recognized by the α-Karyopherin (Kapα) through its nuclear localization signal (NLS) consisting of three positive residues that are not in a continuous sequence. The Importin system can distinguish between FABP loaded with activating and non-activating compounds. In the present study, we introduced molecular dynamics as a tool for clarifying the mechanism by which FABP4, loaded with activating ligand (linoleate) is recognized by Kapα. In the first phase, we simulated the complex between KapαΔIBB (termed “Armadillo”) that was crystallized with two NLS hepta-peptides. The trajectory revealed that the crystal-structure orientation of the peptides is rapidly lost and new interactions dominate. Though, the NLS sequence of FABP4 is cryptic, since the functional residues are not in direct sequence, implicating more than one possible conformation. Therefore, four possible docked conformations were generated, in which the NLS of FABP4 is interacting with either the major or the minor sites of Kapα, and the N → C vectors are parallel or anti-parallel. Out of these four basic starting positions, only the FABP4-minor site complex exhibited a large number of contact points. In this complex, the FABP interacts with the minor and the major sites, suppressing the self-inhibitory interaction of the Kapα, rendering it free to react with Kapβ. Finally, we propose that the transportable conformation generated an extended hydrophobic domain which expanded out of the boundary of the FABP4, allowing the loaded linoleate to partially migrate out of the FABP into a joint complex in which the Kapα contributes part of a combined binding pocket.
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Tse A, Verkhivker GM. Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality. J Chem Inf Model 2015; 55:1645-62. [DOI: 10.1021/acs.jcim.5b00240] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Amanda Tse
- Graduate Program in Computational and Data Sciences,
Department of Computational Sciences, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences,
Department of Computational Sciences, Schmid College of Science and
Technology, Chapman University, One University Drive, Orange, California 92866, United States
- Chapman University School of Pharmacy, Irvine, California 92618, United States
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