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Yoon C, Lee EJ, Kim D, Joung S, Kim Y, Jung H, Kim YG, Lee GM. SiMPl-GS: Advancing Cell Line Development via Synthetic Selection Marker for Next-Generation Biopharmaceutical Production. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405593. [PMID: 39105414 DOI: 10.1002/advs.202405593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/24/2024] [Indexed: 08/07/2024]
Abstract
Rapid and efficient cell line development (CLD) process is essential to expedite therapeutic protein development. However, the performance of widely used glutamine-based selection systems is limited by low selection efficiency, stringency, and the inability to select multiple genes. Therefore, an AND-gate synthetic selection system is rationally designed using split intein-mediated protein ligation of glutamine synthetase (GS) (SiMPl-GS). Split sites of the GS are selected using a computational approach and validated with GS-knockout Chinese hamster ovary cells for their potential to enable cell survival in a glutamine-free medium. In CLD, SiMPl-GS outperforms the wild-type GS by selectively enriching high producers. Unlike wild-type GS, SiMPl-GS results in cell pools in which most cells produce high levels of therapeutic proteins. Harnessing orthogonal split intein pairs further enables the selection of four plasmids with a single selection, streamlining multispecific antibody-producing CLD. Taken together, SiMPl-GS is a simple yet effective means to expedite CLD for therapeutic protein production.
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Affiliation(s)
- Chansik Yoon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Eun-Ji Lee
- Biotherapeutics Translational Research Center, KRIBB, Daejeon, 34113, Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, Daejeon, 34141, Republic of Korea
| | - Dongil Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Siyun Joung
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Yujin Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Heungchae Jung
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, Daejeon, 34141, Republic of Korea
- BIO Center, Daejeon Technopark, Daejeon, 34054, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, KRIBB, Daejeon, 34113, Republic of Korea
- Department of Bioprocess Engineering, KRIBB School of Biotechnology, UST, Daejeon, 34141, Republic of Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
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2
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Guarra F, Colombo G. Conformational Dynamics, Energetics, and the Divergent Evolution of Allosteric Regulation: The Case of the Yeast MAPK Family. Chembiochem 2024; 25:e202400175. [PMID: 38775368 DOI: 10.1002/cbic.202400175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/24/2024] [Indexed: 07/06/2024]
Abstract
Allosteric mechanisms provide finely-tuned control over signalling proteins. Proteins of the same family may share high sequence identity and structural similarity but show distinct traits of allosteric control and evolutionary divergent regulation. Revealing the determinants of such properties may be important to understand the molecular bases of different regulatory pathways. Herein, we investigate whether and how evolutionarily-divergent traits of allosteric regulation in homologous proteins can be decoded in terms of internal dynamics and interaction networks that support functionally oriented conformations. In this framework, we start from the comparative analysis of the dynamics and energetics of the yeast MAP Kinases (MAPKs) Fus3 and Kss1 in their native basins. Importantly, distinctive dynamic and energetic stabilization features emerge, which can be related to the two proteins' differential ability to be phosphorylated and engage with the allosteric activator Ste5. We then expanded our study to other evolutionarily-related MAPKs. We show that the dynamical and energetical traits defining the distinct regulatory profiles of Fus3 and Kss1 can be traced along their evolutionary tree. Overall, our approach is able to reconnect (latent) allostery with the principal elements of protein structural stabilization and dynamics, showing how allosteric regulation was encrypted in MAPKs structure well before Ste5 appearance.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italia
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Taramelli 12, 27100, Pavia, Italia
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3
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Fongang B, Wadop YN, Zhu Y, Wagner EJ, Kudlicki A, Rowicka M. Coevolution combined with molecular dynamics simulations provides structural and mechanistic insights into the interactions between the integrator complex subunits. Comput Struct Biotechnol J 2023; 21:5686-5697. [PMID: 38074468 PMCID: PMC10700540 DOI: 10.1016/j.csbj.2023.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/10/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
Finding the 3D structure of large, multi-subunit complexes is difficult, despite recent advances in cryo-EM technology, due to remaining challenges to expressing and purifying subunits. Computational approaches that predict protein-protein interactions, including Direct Coupling Analysis (DCA), represent an attractive alternative for dissecting interactions within protein complexes. However, they are readily applicable only to small proteins due to high computational complexity and a high number of false positives. To solve this problem, we proposed a modified DCA approach, a powerful tool to predict the most likely interfaces of protein complexes. Since our modified approach cannot provide structural and mechanistic details of interacting peptides, we combine it with Molecular Dynamics (MD) simulations. To illustrate this novel approach, we predict interacting domains and structural details of interactions of two Integrator complex subunits, INTS9 and INTS11. Our predictions of interacting residues of INTS9/INTS11 are highly consistent with crystallographic structure. We then expand our procedure to two complexes whose structures are not well-studied: 1) The heterodimer formed by the Cleavage and Polyadenylation Specificity Factor 100-kD (CPSF100) and 73-kD (CPSF73); 2) The heterotrimer formed by INTS4/INTS9/INTS11. Experimental data supports our predictions of interactions within these two complexes, demonstrating that combining DCA and MD simulations is a powerful approach to revealing structural insights of large protein complexes.
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Affiliation(s)
- Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Department of Population Health Sciences, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Yannick N. Wadop
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Yingjie Zhu
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Department of Biochemistry and Biophysics, The University of Rochester Medical Center, Rochester, NY, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
- Informatics Service Center, The University of Texas Medical Branch, Galveston, TX, United States
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, United States
- Institute for Translational Sciences, The University of Texas Medical Branch, Galveston, TX, United States
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4
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Konecki DM, Hamrick S, Wang C, Agosto MA, Wensel TG, Lichtarge O. CovET: A covariation-evolutionary trace method that identifies protein structure-function modules. J Biol Chem 2023; 299:104896. [PMID: 37290531 PMCID: PMC10338321 DOI: 10.1016/j.jbc.2023.104896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023] Open
Abstract
Measuring the relative effect that any two sequence positions have on each other may improve protein design or help better interpret coding variants. Current approaches use statistics and machine learning but rarely consider phylogenetic divergences which, as shown by Evolutionary Trace studies, provide insight into the functional impact of sequence perturbations. Here, we reframe covariation analyses in the Evolutionary Trace framework to measure the relative tolerance to perturbation of each residue pair during evolution. This approach (CovET) systematically accounts for phylogenetic divergences: at each divergence event, we penalize covariation patterns that belie evolutionary coupling. We find that while CovET approximates the performance of existing methods to predict individual structural contacts, it performs significantly better at finding structural clusters of coupled residues and ligand binding sites. For example, CovET found more functionally critical residues when we examined the RNA recognition motif and WW domains. It correlates better with large-scale epistasis screen data. In the dopamine D2 receptor, top CovET residue pairs recovered accurately the allosteric activation pathway characterized for Class A G protein-coupled receptors. These data suggest that CovET ranks highest the sequence position pairs that play critical functional roles through epistatic and allosteric interactions in evolutionarily relevant structure-function motifs. CovET complements current methods and may shed light on fundamental molecular mechanisms of protein structure and function.
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Affiliation(s)
- Daniel M Konecki
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA
| | - Spencer Hamrick
- Chemical, Physical, and Structural Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Melina A Agosto
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Theodore G Wensel
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA
| | - Olivier Lichtarge
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Cancer and Cell Biology Graduate Program, Baylor College of Medicine, Houston, Texas, USA; Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, Texas, USA.
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5
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Hemu X, Chan NY, Liew HT, Hu S, Zhang X, Serra A, Lescar J, Liu CF, Tam JP. Substrate-binding glycine residues are major determinants for hydrolase and ligase activity of plant legumains. THE NEW PHYTOLOGIST 2023; 238:1534-1545. [PMID: 36843268 DOI: 10.1111/nph.18841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Peptide asparaginyl ligases (PALs) are useful tools for precision modifications of proteins and live-cell surfaces by ligating peptides after Asn/Asp (Asx). They share high sequence and structural similarity to plant legumains that are generally known as asparaginyl endopeptidases (AEPs), thus making it challenging to identify PALs from AEPs. In this study, we investigate 875 plant species from algae to seed plants with available sequence data in public databases to identify new PALs. We conducted evolutionary trace analysis on 1500 plant legumains, including eight known PALs, to identify key residues that could differentiate ligases and proteases, followed by recombinant expression and functional validation of 16 novel legumains. Previously, we showed that the substrate-binding sequences flanking the catalytic site can strongly influence the enzymatic direction of a legumain and which we named as ligase-activity determinants (LADs). Here, we show that two conserved substrate-binding Gly residues of LADs are critical, but negative determinants for ligase activity. Our results suggest that specific glycine residues are molecular determinants to identify PALs and AEPs as two different legumain subfamilies, accounting for c. 1% and 88%, respectively.
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Affiliation(s)
- Xinya Hemu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Ning-Yu Chan
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Heng Tai Liew
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Side Hu
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Xiaohong Zhang
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - Aida Serra
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- Neuroscience Area, +Pec Proteomics Research Group (+PPRG), Faculty of Medicine, Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRB Lleida), University of Lleida, Av. Rovira Roure, 80, Lleida, 25198, Spain
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
| | - Chuan-Fa Liu
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
| | - James P Tam
- School of Biological Sciences, Synzymes and Natural Products Center (SYNC), Nanyang Technological University, 60 Nanyang Drive, Singapore City, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore City, 637921, Singapore
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6
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González-Gordo S, López-Jaramillo J, Palma JM, Corpas FJ. Soybean ( Glycine max L.) Lipoxygenase 1 (LOX 1) Is Modulated by Nitric Oxide and Hydrogen Sulfide: An In Vitro Approach. Int J Mol Sci 2023; 24:ijms24098001. [PMID: 37175708 PMCID: PMC10178856 DOI: 10.3390/ijms24098001] [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: 03/28/2023] [Revised: 04/03/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Hydrogen sulfide (H2S) and nitric oxide (NO) are two relevant signal molecules that can affect protein function throughout post-translational modifications (PTMs) such as persulfidation, S-nitrosation, metal-nitrosylation, and nitration. Lipoxygenases (LOXs) are a group of non-heme iron enzymes involved in a wide range of plant physiological functions including seed germination, plant growth and development, and fruit ripening and senescence. Likewise, LOXs are also involved in the mechanisms of response to diverse environmental stresses. Using purified soybean (Glycine max L.) lipoxygenase type 1 (LOX 1) and nitrosocysteine (CysNO) and sodium hydrosulfide (NaHS) as NO and H2S donors, respectively, the present study reveals that both compounds negatively affect LOX activity, suggesting that S-nitrosation and persulfidation are involved. Mass spectrometric analysis of nitrated soybean LOX 1 using a peroxynitrite (ONOO-) donor enabled us to identify that, among the thirty-five tyrosine residues present in this enzyme, only Y214 was exclusively nitrated by ONOO-. The nitration of Y214 seems to affect its interaction with W500, a residue involved in the substrate binding site. The analysis of the structure 3PZW demonstrates the existence of several tunnels that directly communicate the surface of the protein with different internal cysteines, thus making feasible their potential persulfidation, especially C429 and C127. On the other hand, the CysNO molecule, which is hydrophilic and bulkier than H2S, can somehow be accommodated throughout the tunnel until it reaches C127, thus facilitating its nitrosation. Overall, a large number of potential persulfidation targets and the ease by which H2S can reach them through the diffuse tunneling network could be behind their efficient inhibition.
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Affiliation(s)
- Salvador González-Gordo
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | | | - José M Palma
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008 Granada, Spain
| | - Francisco J Corpas
- Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Profesor Albareda 1, 18008 Granada, Spain
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7
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Rodríguez-Núñez K, Cortés-Monroy A, Serey M, Ensari Y, Davari MD, Bernal C, Martinez R. Modulating Substrate Specificity of Rhizobium sp. Histamine Dehydrogenase through Protein Engineering for Food Quality Applications. Molecules 2023; 28:molecules28093748. [PMID: 37175158 PMCID: PMC10180351 DOI: 10.3390/molecules28093748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Histamine is a biogenic amine found in fish-derived and fermented food products with physiological relevance since its concentration is proportional to food spoilage and health risk for sensitive consumers. There are various analytical methods for histamine quantification from food samples; however, a simple and quick enzymatic detection and quantification method is highly desirable. Histamine dehydrogenase (HDH) is a candidate for enzymatic histamine detection; however, other biogenic amines can change its activity or produce false positive results with an observed substrate inhibition at higher concentrations. In this work, we studied the effect of site saturation mutagenesis in Rhizobium sp. Histamine Dehydrogenase (Rsp HDH) in nine amino acid positions selected through structural alignment analysis, substrate docking, and proximity to the proposed histamine-binding site. The resulting libraries were screened for histamine and agmatine activity. Variants from two libraries (positions 72 and 110) showed improved histamine/agmatine activity ratio, decreased substrate inhibition, and maintained thermal resistance. In addition, activity characterization of the identified Phe72Thr and Asn110Val HDH variants showed a clear substrate inhibition curve for histamine and modified kinetic parameters. The observed maximum velocity (Vmax) increased for variant Phe72Thr at the cost of an increased value for the Michaelis-Menten constant (Km) for histamine. The increased Km value, decreased substrate inhibition, and biogenic amine interference observed for variant Phe72Thr support a tradeoff between substrate affinity and substrate inhibition in the catalytic mechanism of HDHs. Considering this tradeoff for future enzyme engineering of HDH could lead to breakthroughs in performance increases and understanding of this enzyme class.
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Affiliation(s)
- Karen Rodríguez-Núñez
- Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile
| | - Alejandra Cortés-Monroy
- Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile
| | - Marcela Serey
- Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile
| | - Yunus Ensari
- Department of Bioengineering, Faculty of Engineering and Architecture, Kafkas University, Kars 36000, Turkey
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle, Germany
| | - Claudia Bernal
- Instituto de Investigación Multidisciplinaria en Ciencia y Tecnología, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile
| | - Ronny Martinez
- Departamento de Ingeniería en Alimentos, Universidad de La Serena, Av. Raúl Bitrán 1305, La Serena 1720010, Chile
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8
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Marciano DC, Wang C, Hsu TK, Bourquard T, Atri B, Nehring RB, Abel NS, Bowling EA, Chen TJ, Lurie PD, Katsonis P, Rosenberg SM, Herman C, Lichtarge O. Evolutionary action of mutations reveals antimicrobial resistance genes in Escherichia coli. Nat Commun 2022; 13:3189. [PMID: 35680894 PMCID: PMC9184624 DOI: 10.1038/s41467-022-30889-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Since antibiotic development lags, we search for potential drug targets through directed evolution experiments. A challenge is that many resistance genes hide in a noisy mutational background as mutator clones emerge in the adaptive population. Here, to overcome this noise, we quantify the impact of mutations through evolutionary action (EA). After sequencing ciprofloxacin or colistin resistance strains grown under different mutational regimes, we find that an elevated sum of the evolutionary action of mutations in a gene identifies known resistance drivers. This EA integration approach also suggests new antibiotic resistance genes which are then shown to provide a fitness advantage in competition experiments. Moreover, EA integration analysis of clinical and environmental isolates of antibiotic resistant of E. coli identifies gene drivers of resistance where a standard approach fails. Together these results inform the genetic basis of de novo colistin resistance and support the robust discovery of phenotype-driving genes via the evolutionary action of genetic perturbations in fitness landscapes.
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Affiliation(s)
- David C Marciano
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Chen Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Teng-Kuei Hsu
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas Bourquard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Benu Atri
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Clara Analytics Inc., 451 El Camino Real #201, Santa Clara, CA, 95050, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth A Bowling
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Taylor J Chen
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pamela D Lurie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- The Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Molecular & Biomedical Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Structural and Computational Biology & Molecular Biophysics Program, Baylor College of Medicine, Houston, TX, 77030, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Computational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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9
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Cagiada M, Johansson KE, Valanciute A, Nielsen SV, Hartmann-Petersen R, Yang JJ, Fowler DM, Stein A, Lindorff-Larsen K. Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance. Mol Biol Evol 2021; 38:3235-3246. [PMID: 33779753 PMCID: PMC8321532 DOI: 10.1093/molbev/msab095] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Understanding and predicting how amino acid substitutions affect proteins are keys to our basic understanding of protein function and evolution. Amino acid changes may affect protein function in a number of ways including direct perturbations of activity or indirect effects on protein folding and stability. We have analyzed 6,749 experimentally determined variant effects from multiplexed assays on abundance and activity in two proteins (NUDT15 and PTEN) to quantify these effects and find that a third of the variants cause loss of function, and about half of loss-of-function variants also have low cellular abundance. We analyze the structural and mechanistic origins of loss of function and use the experimental data to find residues important for enzymatic activity. We performed computational analyses of protein stability and evolutionary conservation and show how we may predict positions where variants cause loss of activity or abundance. In this way, our results link thermodynamic stability and evolutionary conservation to experimental studies of different properties of protein fitness landscapes.
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Affiliation(s)
- Matteo Cagiada
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer E Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Audrone Valanciute
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V Nielsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Amelie Stein
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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10
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Millan CR, Francis M, Khandelwal NK, Thompson VF, Thaker TM, Tomasiak TM. A Conserved Motif in Intracellular Loop 1 Stabilizes the Outward-Facing Conformation of TmrAB. J Mol Biol 2021; 433:166834. [PMID: 33524413 DOI: 10.1016/j.jmb.2021.166834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/05/2023]
Abstract
The ATP binding cassette (ABC) family of transporters moves small molecules (lipids, sugars, peptides, drugs, nutrients) across membranes in nearly all organisms. Transport activity requires conformational switching between inward-facing and outward-facing states driven by ATP-dependent dimerization of two nucleotide binding domains (NBDs). The mechanism that connects ATP binding and hydrolysis in the NBDs to conformational changes in a substrate binding site in the transmembrane domains (TMDs) is currently an outstanding question. Here we use sequence coevolution analyses together with biochemical characterization to investigate the role of a highly conserved region in intracellular loop 1 we define as the GRD motif in coordinating domain rearrangements in the heterodimeric peptide exporter from Thermus thermophilus, TmrAB. Mutations in the GRD motif alter ATPase activity as well as transport. Disulfide crosslinking, evolutionary trace, and evolutionary coupling analysis reveal that these effects are likely due to the destabilization of a network in which the GRD motif in TmrA bridges residues of the Q-loop, X-loop, and ABC motif in the NBDs to residues in the TmrAB peptide substrate binding site, thus providing an avenue for conformational coupling. We further find that disruption of this network in TmrA versus TmrB has different functional consequences, hinting at an intrinsic asymmetry in heterodimeric ABC transporters extending beyond that of the NBDs. These results support a mechanism in which the GRD motifs help coordinate a transition to an outward open conformation, and each half of the transporter likely plays a different role in the conformational cycle of TmrAB.
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Affiliation(s)
- Cinthia R Millan
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Martina Francis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | | | - Valery F Thompson
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Tarjani M Thaker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.
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11
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Diallo S, Shahbaaz M, Torto B, Christoffels A, Masiga D, Getahun MN. Cellular and Molecular Targets of Waterbuck Repellent Blend Odors in Antennae of Glossina fuscipes fuscipes Newstead, 1910. Front Cell Neurosci 2020; 14:137. [PMID: 32581714 PMCID: PMC7283967 DOI: 10.3389/fncel.2020.00137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/22/2020] [Indexed: 01/20/2023] Open
Abstract
Insects that transmit many of the world's deadliest animal diseases, for instance trypanosomosis, find their suitable hosts and avoid non-preferred hosts mostly through olfactory cues. The waterbuck repellent blend (WRB) comprising geranylacetone, guaiacol, pentanoic acid, and δ-octalactone derived from waterbuck skin odor is a repellent to some savannah-adapted tsetse flies and reduces trap catches of riverine species. However, the cellular and molecular mechanisms associated with detection and coding of the repellent odors remain to be elucidated. Here, we demonstrated that WRB inhibited blood feeding in both Glossina pallidipes Austen, 1903 and Glossina fuscipes fuscipes Newstead, 1910. Using the DREAM (Deorphanization of Receptors based on Expression Alterations in odorant receptor mRNA levels) technique, combined with ortholog comparison and molecular docking, we predicted the putative odorant receptors (ORs) for the WRB in G. f. fuscipes, a non-model insect. We show that exposure of G. f. fuscipes in vivo to WRB odorant resulted in up- and downregulation of mRNA transcript of several ORs. The WRB component with strong feeding inhibition altered mRNA transcript differently as compared to an attractant odor, showing these two odors of opposing valence already segregate at the cellular and molecular levels. Furthermore, molecular dynamics simulations demonstrated that the predicted ligand-OR binding pockets consisted mostly of hydrophobic residues with a few hydrogen bonds but a stable interaction. Finally, our electrophysiological response showed the olfactory sensory neurons of G. f. fuscipes tuned to the tsetse repellent components in different sensitivity and selectivity.
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Affiliation(s)
- Souleymane Diallo
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya.,South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya.,Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Daniel Masiga
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Merid N Getahun
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
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12
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An Evolutionary Marker of the Ribokinase Superfamily Is Responsible for Zinc-Mediated Regulation of Human Pyridoxal Kinase. Catalysts 2020. [DOI: 10.3390/catal10050555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The ribokinase superfamily catalyzes the phosphorylation of a vast diversity of substrates, and its members are characterized by the conservation of a common structural fold along with highly conserved sequence motifs responsible for phosphoryl transfer (GXGD) and stabilization of the metal-nucleotide complex (NXXE). Recently, a third motif (HXE) exclusive from ADP-dependent enzymes was identified, with its glutamic acid participating in water-mediated interactions with the metal-nucleotide complex and in stabilization of the ternary complex during catalysis. In this work, we bioinformatically determine that the aspartic acid of another motif (DPV), exclusively found in hydroxyethyl thiazole (THZK), hydroxymethyl pyrimidine (HMPK) and pyridoxal kinases (PLK), is structurally equivalent to the acidic residue in the HXE motif. Moreover, this residue is highly conserved among all ribokinase superfamily members. To determine whether the functional role of the DPV motif is similar to the HXE motif, we employed molecular dynamics simulations using crystal structures of phosphoryl donor substrate-complexed THZK and PLK, showing that its aspartic acid participated in water-mediated or direct interactions with the divalent metal of the metal-nucleotide complex. Lastly, enzyme kinetic assays on human PLK, an enzyme that utilizes zinc, showed that site-directed mutagenesis of the aspartic acid from the DPV motif abolishes the inhibition of this enzyme by increasing free zinc concentrations. Altogether, our results highlight that the DPV and HXE motifs are evolutionary markers of the functional and structural divergence of the ribokinase superfamily and evidence the role of the DPV motif in the interaction with both free and nucleotide-complexed divalent metals in the binding site of these enzymes.
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13
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Goutham S, Kumari I, Pally D, Singh A, Ghosh S, Akhter Y, Bhat R. Mutually exclusive locales for N-linked glycans and disorder in human glycoproteins. Sci Rep 2020; 10:6040. [PMID: 32269229 PMCID: PMC7142085 DOI: 10.1038/s41598-020-61427-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/30/2020] [Indexed: 11/08/2022] Open
Abstract
Several post-translational protein modifications lie predominantly within regions of disorder: the biased localization has been proposed to expand the binding versatility of disordered regions. However, investigating a representative dataset of 500 human N-glycoproteins, we observed the sites of N-linked glycosylations or N-glycosites, to be predominantly present in the regions of predicted order. When compared with disordered stretches, ordered regions were not found to be enriched for asparagines, serines and threonines, residues that constitute the sequon signature for conjugation of N-glycans. We then investigated the basis of mutual exclusivity between disorder and N-glycosites on the basis of amino acid distribution: when compared with control ordered residue stretches without any N-glycosites, residue neighborhoods surrounding N-glycosites showed a depletion of bulky, hydrophobic and disorder-promoting amino acids and an enrichment for flexible and accessible residues that are frequently found in coiled structures. When compared with control disordered residue stretches without any N-glycosites, N-glycosite neighborhoods were depleted of charged, polar, hydrophobic and flexible residues and enriched for aromatic, accessible and order-promoting residues with a tendency to be part of coiled and β structures. N-glycosite neighborhoods also showed greater phylogenetic conservation among amniotes, compared with control ordered regions, which in turn were more conserved than disordered control regions. Our results lead us to propose that unique primary structural compositions and differential propensities for evolvability allowed for the mutual spatial exclusion of N-glycosite neighborhoods and disordered stretches.
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Affiliation(s)
- Shyamili Goutham
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Indu Kumari
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, District-Kangra, Shahpur, Himachal Pradesh, 176206, India
| | - Dharma Pally
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Alvina Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Sujasha Ghosh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Ramray Bhat
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Sciences, Bangalore, 560012, India.
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14
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Fongang B, Cunningham KA, Rowicka M, Kudlicki A. Coevolution of Residues Provides Evidence of a Functional Heterodimer of 5-HT 2AR and 5-HT 2CR Involving Both Intracellular and Extracellular Domains. Neuroscience 2019; 412:48-59. [PMID: 31158438 PMCID: PMC7299066 DOI: 10.1016/j.neuroscience.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/02/2019] [Accepted: 05/07/2019] [Indexed: 10/26/2022]
Abstract
Serotonin is a neurotransmitter that plays a role in regulating activities such as sleep, appetite, mood and substance abuse disorders; serotonin receptors 5-HT2AR and 5-HT2CR are active within pathways associated with substance abuse. It has been suggested that 5-HT2AR and 5-HT2CR may form a dimer that affects behavioral processes. Here we study the coevolution of residues in 5-HT2AR and 5-HT2CR to identify potential interactions between residues in both proteins. Coevolution studies can detect protein interactions, and since the thus uncovered interactions are subject to evolutionary pressure, they are likely functional. We assessed the significance of the 5-HT2AR/5-HT2CR interactions using randomized phylogenetic trees and found the coevolution significant (p-value = 0.01). We also discuss how co-expression of the receptors suggests the predicted interaction is functional. Finally, we analyze how several single nucleotide polymorphisms for the 5-HT2AR and 5-HT2CR genes affect their interaction. Our findings are the first to characterize the binding interface of 5-HT2AR/5-HT2CR and indicate a correlation between this interface and location of SNPs in both proteins.
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MESH Headings
- Animals
- Databases, Genetic
- Evolution, Molecular
- Papio anubis
- Phosphorylation
- Receptor, Serotonin, 5-HT2A/genetics
- Receptor, Serotonin, 5-HT2A/metabolism
- Receptor, Serotonin, 5-HT2C/genetics
- Receptor, Serotonin, 5-HT2C/metabolism
- Transcriptome
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Affiliation(s)
- Bernard Fongang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UTHSCSA, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, UTHSCSA, San Antonio, TX 78229, USA; Department of Epidemiology and Biostatistics, UTHSCSA, San Antonio, TX 78229, USA.
| | - Kathryn A Cunningham
- Center for Addiction Research and Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrzej Kudlicki
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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15
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Ban X, Lahiri P, Dhoble AS, Li D, Gu Z, Li C, Cheng L, Hong Y, Li Z, Kaustubh B. Evolutionary Stability of Salt Bridges Hints Its Contribution to Stability of Proteins. Comput Struct Biotechnol J 2019; 17:895-903. [PMID: 31333816 PMCID: PMC6620738 DOI: 10.1016/j.csbj.2019.06.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
The contribution of newly designed salt bridges to protein stabilization remains controversial even today. In order to solve this problem, we investigated salt bridges from two aspects: spatial distribution and evolutionary characteristics of salt bridges. Firstly, we analyzed spatial distribution of salt bridges in proteins, elucidating the basic requirements of forming salt bridges. Then, from an evolutionary point of view, the evolutionary characteristics of salt bridges as well as their neighboring residues were investigated in our study. The results demonstrate that charged residues appear more frequently than other neutral residues at certain positions of sequence even under evolutionary pressure, which are able to form electrostatic interactions that could increase the evolutionary stability of corresponding amino acid regions, enhancing their importance to stability of proteins. As a corollary, we conjectured that the newly designed salt bridges with more contribution to proteins, not only, are qualified spatial distribution of salt bridges, but also, are needed to further increase the evolutionary stability of corresponding amino acid regions. Based on analysis, the 8 mutations were accordingly constructed in the 1,4-α-glucan branching enzyme (EC 2.4.1.18, GBE) from Geobacillus thermoglucosidans STB02, of which 7 mutations improved thermostability of GBE. The enhanced thermostability of 7 mutations might be a result of additional salt bridges on residue positions that at least one of amino acids positions is conservative, improving their contribution of stabilization to proteins.
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Affiliation(s)
- Xiaofeng Ban
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Pratik Lahiri
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, IL-61801, USA
| | - Abhishek S. Dhoble
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, IL-61801, USA
| | - Dan Li
- The Second Military Medical University, Shanghai, China
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Caiming Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Li Cheng
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yan Hong
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Bhalerao Kaustubh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, IL-61801, USA
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16
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Batra S, Corcoran J, Zhang DD, Pal P, K.P. U, Kulkarni R, Löfstedt C, Sowdhamini R, Olsson SB. A Functional Agonist of Insect Olfactory Receptors: Behavior, Physiology and Structure. Front Cell Neurosci 2019; 13:134. [PMID: 31110474 PMCID: PMC6501728 DOI: 10.3389/fncel.2019.00134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/19/2019] [Indexed: 12/26/2022] Open
Abstract
Chemical signaling is ubiquitous and employs a variety of receptor types to detect the cacophony of molecules relevant for each living organism. Insects, our most diverse taxon, have evolved unique olfactory receptors with as little as 10% sequence identity between receptor types. We have identified a promiscuous volatile, 2-methyltetrahydro-3-furanone (coffee furanone), that elicits chemosensory and behavioral activity across multiple insect orders and receptors. In vivo and in vitro physiology showed that coffee furanone was detected by roughly 80% of the recorded neurons expressing the insect-specific olfactory receptor complex in the antenna of Drosophila melanogaster, at concentrations similar to other known, and less promiscuous, ligands. Neurons expressing specialized receptors, other chemoreceptor types, or mutants lacking the complex entirely did not respond to this compound. This indicates that coffee furanone is a promiscuous ligand for the insect olfactory receptor complex itself and did not induce non-specific cellular responses. In addition, we present homology modeling and docking studies with selected olfactory receptors that suggest conserved interaction regions for both coffee furanone and known ligands. Apart from its physiological activity, this known food additive elicits a behavioral response for several insects, including mosquitoes, flies, and cockroaches. A broad-scale behaviorally active molecule non-toxic to humans thus has significant implications for health and agriculture. Coffee furanone serves as a unique tool to unlock molecular, physiological, and behavioral relationships across this diverse receptor family and animal taxa.
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Affiliation(s)
- Srishti Batra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | | | - Dan-Dan Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Pramit Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Umesh K.P.
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Renuka Kulkarni
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | | | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Shannon B. Olsson
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
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17
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Misiura M, Wang Q, Cheung MS, Kolomeisky AB. Theoretical Investigations of the Role of Mutations in Dynamics of Kinesin Motor Proteins. J Phys Chem B 2018; 122:4653-4661. [PMID: 29630822 DOI: 10.1021/acs.jpcb.8b00830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Motor proteins are active enzymatic molecules that are critically important for a variety of biological phenomena. It is known that some neurodegenerative diseases are caused by specific mutations in motor proteins that lead to their malfunctioning. Hereditary spastic paraplegia is one of such diseases, and it is associated with the mutations in the neuronal conventional kinesin gene, producing the decreased speed and processivity of this motor protein. Despite the importance of this problem, there is no clear understanding on the role of mutations in modifying dynamic properties of motor proteins. In this work, we investigate theoretically the molecular basis for negative effects of two specific mutations, N256S and R280S, on the dynamics of kinesin motor proteins. We hypothesize that these mutations might accelerate the adenosine triphosphate (ATP) release by increasing the probability of open conformations for the ATP-binding pocket. Our approach is based on the use of coarse-grained structure-based molecular dynamics simulations to analyze the conformational changes and chemical transitions in the kinesin molecule, which is also supplemented by investigation of a mesoscopic discrete-state stochastic model. Computer simulations suggest that mutations N256S and R280S can decrease the free energy difference between open and closed biochemical states, making the open conformation more stable and the ATP release faster, which is in agreement with our hypothesis. Furthermore, we show that in the case of N256S mutation, this effect is caused by disruption of interactions between α helix and switch I and loop L11 structural elements. Our computational results are qualitatively supported by the explicit analysis of the discrete-state stochastic model.
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Affiliation(s)
| | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston , Texas 77204 , United States
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18
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Atas H, Tuncbag N, Doğan T. Phylogenetic and Other Conservation-Based Approaches to Predict Protein Functional Sites. Methods Mol Biol 2018; 1762:51-69. [PMID: 29594767 DOI: 10.1007/978-1-4939-7756-7_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Proteins use their functional regions to exploit various activities, including binding to other proteins, nucleic acids, or drugs. Functional sites of the proteins have a tendency to be more conserved than the rest of the protein surface. Therefore, detection of the conserved residues using phylogenetic analysis is a general approach to predict functionally critical residues. In this chapter, we describe some of the available methods to predict functional sites and demonstrate a complete pipeline with tool alternatives at several steps. We explain the standard procedure and all intermediate stages including homology detection with BLAST search, multiple sequence alignment (MSA) and the construction of a phylogenetic tree for a given query sequence. Additionally, we demonstrate the prediction results of these methods on a case study. Finally, we discuss the possible challenges and bottlenecks throughout the pipeline. Our step-by-step description about the functional site prediction could be a helpful resource for the researchers interested in finding protein functional sites, to be used in drug discovery research.
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Affiliation(s)
- Heval Atas
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, 06800, Turkey.,Cancer Systems Biology Laboratory (CanSyL), METU, Ankara, 06800, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, 06800, Turkey.,Cancer Systems Biology Laboratory (CanSyL), METU, Ankara, 06800, Turkey
| | - Tunca Doğan
- Department of Health Informatics, Graduate School of Informatics, METU, Ankara, 06800, Turkey. .,Cancer Systems Biology Laboratory (CanSyL), METU, Ankara, 06800, Turkey. .,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, CB10 1SD, UK.
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19
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Medvedeva IV, Demenkov PS, Ivanisenko VA. SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes. J Bioinform Comput Biol 2017; 15:1650044. [PMID: 28110602 DOI: 10.1142/s021972001650044x] [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] [Indexed: 11/18/2022]
Abstract
Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/ .
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Affiliation(s)
- Irina V Medvedeva
- * Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyeva 10, Novosibirsk, 630090, Russia.,† Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russia
| | - Pavel S Demenkov
- * Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyeva 10, Novosibirsk, 630090, Russia.,† Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russia
| | - Vladimir A Ivanisenko
- * Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentyeva 10, Novosibirsk, 630090, Russia
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20
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Rigden DJ, Fernández-Suárez XM, Galperin MY. The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic Acids Res 2016; 44:D1-6. [PMID: 26740669 PMCID: PMC4702933 DOI: 10.1093/nar/gkv1356] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 01/21/2023] Open
Abstract
The 2016 Database Issue of Nucleic Acids Research starts with overviews of the resources provided by three major bioinformatics centers, the U.S. National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EMBL-EBI) and Swiss Institute for Bioinformatics (SIB). Also included are descriptions of 62 new databases and updates on 95 databases that have been previously featured in NAR plus 17 previously described elsewhere. A number of papers in this issue deal with resources on nucleic acids, including various kinds of non-coding RNAs and their interactions, molecular dynamics simulations of nucleic acid structure, and two databases of super-enhancers. The protein database section features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of resources on pathways, metabolomics and metabolic modeling. This issue also includes updates on popular metagenomics resources, such as MG-RAST, EBI Metagenomics, and probeBASE, as well as a newly compiled Human Pan-Microbe Communities database. A significant fraction of the new and updated databases are dedicated to the genetic basis of disease, primarily cancer, and various aspects of drug research, including resources for patented drugs, their side effects, withdrawn drugs, and potential drug targets. A further six papers present updated databases of various antimicrobial and anticancer peptides. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/). The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been updated with the addition of 88 new resources and removal of 23 obsolete websites, which brought the current listing to 1685 databases.
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Affiliation(s)
- Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | | | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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