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Saunders JW, Damry AM, Vongsouthi V, Spence MA, Frkic RL, Gomez C, Yates PA, Matthews DS, Tokuriki N, McLeod MD, Jackson CJ. Increasing the Soluble Expression and Whole-Cell Activity of the Plastic-Degrading Enzyme MHETase through Consensus Design. Biochemistry 2024; 63:1663-1673. [PMID: 38885634 DOI: 10.1021/acs.biochem.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The mono(2-hydroxyethyl) terephthalate hydrolase (MHETase) from Ideonella sakaiensis carries out the second step in the enzymatic depolymerization of poly(ethylene terephthalate) (PET) plastic into the monomers terephthalic acid (TPA) and ethylene glycol (EG). Despite its potential industrial and environmental applications, poor recombinant expression of MHETase has been an obstacle to its industrial application. To overcome this barrier, we developed an assay allowing for the medium-throughput quantification of MHETase activity in cell lysates and whole-cell suspensions, which allowed us to screen a library of engineered variants. Using consensus design, we generated several improved variants that exhibit over 10-fold greater whole-cell activity than wild-type (WT) MHETase. This is revealed to be largely due to increased soluble expression, which biochemical and structural analysis indicates is due to improved protein folding.
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Affiliation(s)
- Jake W Saunders
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Adam M Damry
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Rebecca L Frkic
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Patrick A Yates
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dana S Matthews
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Malcolm D McLeod
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Hong L, Kortemme T. An integrative approach to protein sequence design through multiobjective optimization. PLoS Comput Biol 2024; 20:e1011953. [PMID: 38991035 PMCID: PMC11265717 DOI: 10.1371/journal.pcbi.1011953] [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: 02/28/2024] [Revised: 07/23/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
With recent methodological advances in the field of computational protein design, in particular those based on deep learning, there is an increasing need for frameworks that allow for coherent, direct integration of different models and objective functions into the generative design process. Here we demonstrate how evolutionary multiobjective optimization techniques can be adapted to provide such an approach. With the established Non-dominated Sorting Genetic Algorithm II (NSGA-II) as the optimization framework, we use AlphaFold2 and ProteinMPNN confidence metrics to define the objective space, and a mutation operator composed of ESM-1v and ProteinMPNN to rank and then redesign the least favorable positions. Using the two-state design problem of the foldswitching protein RfaH as an in-depth case study, and PapD and calmodulin as examples of higher-dimensional design problems, we show that the evolutionary multiobjective optimization approach leads to significant reduction in the bias and variance in RfaH native sequence recovery, compared to a direct application of ProteinMPNN. We suggest that this improvement is due to three factors: (i) the use of an informative mutation operator that accelerates the sequence space exploration, (ii) the parallel, iterative design process inherent to the genetic algorithm that improves upon the ProteinMPNN autoregressive sequence decoding scheme, and (iii) the explicit approximation of the Pareto front that leads to optimal design candidates representing diverse tradeoff conditions. We anticipate this approach to be readily adaptable to different models and broadly relevant for protein design tasks with complex specifications.
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Affiliation(s)
- Lu Hong
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
- Quantitative Biosciences Institute, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
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3
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Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K. High-throughput system for the thermostability analysis of proteins. Protein Sci 2024; 33:e5029. [PMID: 38801228 PMCID: PMC11129621 DOI: 10.1002/pro.5029] [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: 03/28/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Thermal stability of proteins is a primary metric for evaluating their physical properties. Although researchers attempted to predict it using machine learning frameworks, their performance has been dependent on the quality and quantity of published data. This is due to the technical limitation that thermodynamic characterization of protein denaturation by fluorescence or calorimetry in a high-throughput manner has been challenging. Obtaining a melting curve that derives solely from the target protein requires laborious purification, making it far from practical to prepare a hundred or more samples in a single workflow. Here, we aimed to overcome this throughput limitation by leveraging the high protein secretion efficacy of Brevibacillus and consecutive treatment with plate-scale purification methodologies. By handling the entire process of expression, purification, and analysis on a per-plate basis, we enabled the direct observation of protein denaturation in 384 samples within 4 days. To demonstrate a practical application of the system, we conducted a comprehensive analysis of 186 single mutants of a single-chain variable fragment of nivolumab, harvesting the melting temperature (Tm) ranging from -9.3 up to +10.8°C compared to the wild-type sequence. Our findings will allow for data-driven stabilization in protein design and streamlining the rational approaches.
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Affiliation(s)
- Sae Ito
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
| | - Ryo Matsunaga
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
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4
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Prakash A, Li Z, Chirasani VR, Rasquinha JA, Valentin NH, Hubbard GB, Yin G, Dohlman HG, Campbell SL. Molecular and Functional Profiling of Gαi as an Intracellular pH Sensor. RESEARCH SQUARE 2024:rs.3.rs-4203924. [PMID: 38746411 PMCID: PMC11092800 DOI: 10.21203/rs.3.rs-4203924/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Heterotrimeric G proteins (Gα, Gβ and Gγ) act downstream of G-protein-coupled receptors (GPCRs) to mediate signaling pathways that regulate various physiological processes and human disease conditions. Previously, human Gαi and its yeast homolog Gpa1 have been reported to function as intracellular pH sensors, yet the pH sensing capabilities of Gαi and the underlying mechanism remain to be established. Herein, we identify a pH sensing network within Gαi, and evaluate the consequences of pH modulation on the structure and stability of the G-protein. We find that changes over the physiological pH range significantly alter the structure and stability of Gαi-GDP, with the protein undergoing a disorder-to-order transition as the pH is raised from 6.8 to 7.5. Further, we find that modulation of intracellular pH in HEK293 cells regulates Gαi-Gβγ release. Identification of key residues in the pH-sensing network allowed the generation of low pH mimetics that attenuate Gαi-Gβγ release. Our findings, taken together, indicate that pH-dependent structural changes in Gαi alter the agonist-mediated Gβγ dissociation necessary for proper signaling.
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Affiliation(s)
- Ajit Prakash
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zijian Li
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Venkata R. Chirasani
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhi A. Rasquinha
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie H. Valentin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Garrett B. Hubbard
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Henrik G. Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Dieckhaus H, Brocidiacono M, Randolph NZ, Kuhlman B. Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proc Natl Acad Sci U S A 2024; 121:e2314853121. [PMID: 38285937 PMCID: PMC10861915 DOI: 10.1073/pnas.2314853121] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/26/2023] [Indexed: 01/31/2024] Open
Abstract
Amino acid mutations that lower a protein's thermodynamic stability are implicated in numerous diseases, and engineered proteins with enhanced stability can be important in research and medicine. Computational methods for predicting how mutations perturb protein stability are, therefore, of great interest. Despite recent advancements in protein design using deep learning, in silico prediction of stability changes has remained challenging, in part due to a lack of large, high-quality training datasets for model development. Here, we describe ThermoMPNN, a deep neural network trained to predict stability changes for protein point mutations given an initial structure. In doing so, we demonstrate the utility of a recently released megascale stability dataset for training a robust stability model. We also employ transfer learning to leverage a second, larger dataset by using learned features extracted from ProteinMPNN, a deep neural network trained to predict a protein's amino acid sequence given its three-dimensional structure. We show that our method achieves state-of-the-art performance on established benchmark datasets using a lightweight model architecture that allows for rapid, scalable predictions. Finally, we make ThermoMPNN readily available as a tool for stability prediction and design.
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Affiliation(s)
- Henry Dieckhaus
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC27599
| | - Michael Brocidiacono
- Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Eshelman School of Pharmacy, Chapel Hill, NC27599
| | - Nicholas Z. Randolph
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Department of Bioinformatics and Computational Biology, University of North Carolina School of Medicine, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC27599
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Sharkia R, Jain S, Mahajnah M, Habib C, Azem A, Al-Shareef W, Zalan A. PTRH2 Gene Variants: Recent Review of the Phenotypic Features and Their Bioinformatics Analysis. Genes (Basel) 2023; 14:genes14051031. [PMID: 37239392 DOI: 10.3390/genes14051031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Peptidyl-tRNA hydrolase 2 (PTRH2) is an evolutionarily highly conserved mitochondrial protein. The biallelic mutations in the PTRH2 gene have been suggested to cause a rare autosomal recessive disorder characterized by an infantile-onset multisystem neurologic endocrine and pancreatic disease (IMNEPD). Patients with IMNEPD present varying clinical manifestations, including global developmental delay associated with microcephaly, growth retardation, progressive ataxia, distal muscle weakness with ankle contractures, demyelinating sensorimotor neuropathy, sensorineural hearing loss, and abnormalities of thyroid, pancreas, and liver. In the current study, we conducted an extensive literature review with an emphasis on the variable clinical spectrum and genotypes in patients. Additionally, we reported on a new case with a previously documented mutation. A bioinformatics analysis of the various PTRH2 gene variants was also carried out from a structural perspective. It appears that the most common clinical characteristics among all patients include motor delay (92%), neuropathy (90%), distal weakness (86.4%), intellectual disability (84%), hearing impairment (80%), ataxia (79%), and deformity of head and face (~70%). The less common characteristics include hand deformity (64%), cerebellar atrophy/hypoplasia (47%), and pancreatic abnormality (35%), while the least common appear to be diabetes mellitus (~30%), liver abnormality (~22%), and hypothyroidism (16%). Three missense mutations were revealed in the PTRH2 gene, the most common one being Q85P, which was shared by four different Arab communities and was presented in our new case. Moreover, four different nonsense mutations in the PTRH2 gene were detected. It may be concluded that disease severity depends on the PTRH2 gene variant, as most of the clinical features are manifested by nonsense mutations, while only the common features are presented by missense mutations. A bioinformatics analysis of the various PTRH2 gene variants also suggested the mutations to be deleterious, as they seem to disrupt the structural confirmation of the enzyme, leading to loss of stability and functionality.
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Affiliation(s)
- Rajech Sharkia
- Unit of Human Biology and Genetics, Triangle Regional Research and Development Center, Kfar Qari 30075, Israel
- Unit of Natural Sciences, Beit-Berl Academic College, Beit-Berl 4490500, Israel
| | - Sahil Jain
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Muhammad Mahajnah
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
- Child Neurology and Development Center, Hillel Yaffe Medical Center, Hadera 38100, Israel
| | - Clair Habib
- Genetics Institute, Rambam Health Care Campus, Haifa 31096, Israel
| | - Abdussalam Azem
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Wasif Al-Shareef
- Unit of Human Biology and Genetics, Triangle Regional Research and Development Center, Kfar Qari 30075, Israel
| | - Abdelnaser Zalan
- Unit of Human Biology and Genetics, Triangle Regional Research and Development Center, Kfar Qari 30075, Israel
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Hernandez CC, Shen Y, Hu N, Shen W, Narayanan V, Ramsey K, He W, Zou L, Macdonald RL. GABRG2 Variants Associated with Febrile Seizures. Biomolecules 2023; 13:414. [PMID: 36979350 PMCID: PMC10046037 DOI: 10.3390/biom13030414] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Febrile seizures (FS) are the most common form of epilepsy in children between six months and five years of age. FS is a self-limited type of fever-related seizure. However, complicated prolonged FS can lead to complex partial epilepsy. We found that among the GABAA receptor subunit (GABR) genes, most variants associated with FS are harbored in the γ2 subunit (GABRG2). Here, we characterized the effects of eight variants in the GABAA receptor γ2 subunit on receptor biogenesis and channel function. Two-thirds of the GABRG2 variants followed the expected autosomal dominant inheritance in FS and occurred as missense and nonsense variants. The remaining one-third appeared as de novo in the affected probands and occurred only as missense variants. The loss of GABAA receptor function and dominant negative effect on GABAA receptor biogenesis likely caused the FS phenotype. In general, variants in the GABRG2 result in a broad spectrum of phenotypic severity, ranging from asymptomatic, FS, genetic epilepsy with febrile seizures plus (GEFS+), and Dravet syndrome individuals. The data presented here support the link between FS, epilepsy, and GABRG2 variants, shedding light on the relationship between the variant topological occurrence and disease severity.
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Affiliation(s)
- Ciria C. Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanwen Shen
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Wen He
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Liping Zou
- Department of Pediatrics, Seventh Medical Center of Chinese PLA General Hospital, Beijing 100010, China
| | - Robert L. Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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