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Kim SM, Kang SH, Jeon BW, Kim YH. Tunnel engineering of gas-converting enzymes for inhibitor retardation and substrate acceleration. BIORESOURCE TECHNOLOGY 2024; 394:130248. [PMID: 38158090 DOI: 10.1016/j.biortech.2023.130248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Carbon monoxide dehydrogenase (CODH), formate dehydrogenase (FDH), hydrogenase (H2ase), and nitrogenase (N2ase) are crucial enzymatic catalysts that facilitate the conversion of industrially significant gases such as CO, CO2, H2, and N2. The tunnels in the gas-converting enzymes serve as conduits for these low molecular weight gases to access deeply buried catalytic sites. The identification of the substrate tunnels is imperative for comprehending the substrate selectivity mechanism underlying these gas-converting enzymes. This knowledge also holds substantial value for industrial applications, particularly in addressing the challenges associated with separation and utilization of byproduct gases. In this comprehensive review, we delve into the emerging field of tunnel engineering, presenting a range of approaches and analyses. Additionally, we propose methodologies for the systematic design of enzymes, with the ultimate goal of advancing protein engineering strategies.
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Affiliation(s)
- Suk Min Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
| | - Sung Heuck Kang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea; Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.
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Valdez-Solana MA, Ventura-García EK, Corral-Guerrero IA, Guzmán de Casa A, Avitia-Domínguez C, Téllez-Valencia A, Sierra-Campos E. In Silico Characterization of the Physicochemical and Biological Properties of the Pink ( Pleurotus djamor var. salmoneostramineus) Oyster Mushroom Chromoprotein. Bioinform Biol Insights 2023; 17:11779322231154139. [PMID: 36776961 PMCID: PMC9912552 DOI: 10.1177/11779322231154139] [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: 08/31/2022] [Accepted: 01/09/2023] [Indexed: 02/11/2023] Open
Abstract
Cap color is an important commercial trait for oyster mushrooms. Various pigment constituents determine a diverse color. However, the pigments of oyster mushrooms are still ambiguous. The pink oyster mushroom (Pleurotus salmoneostramineus or Pleurotus djamor) chromoprotein is one of the few proteins belonging to this fungus that has a record of its sequence of amino acid residues. However, even though there are studies about this chromoprotein isolation, purification, and crystallization, the current information focused on its 3-dimensional model and the cofactor and prosthetic group (3H-indol-3-one) binding sites is unreliable and fragmented. Therefore, in this study, using free online servers such as Prot pi, GalaxyWEB, MIB, and CB-Dock2, a structural analysis and the prediction of its physicochemical and biological properties were conducted, to understand the possible function of this chromoprotein. The obtained results showed that this molecule is a protein with a molecular weight of 23 712.5 Da, an isoelectric point of 7.505, with oligomerization capacity in a dimer and glycation in the Ser6 residue. In addition, the participation of the residues Leu5, Leu8, Lys211, Ala214, and Gln215 in the binding of the prosthetic group to the protein was highlighted; as well as Ser6 and Pro7 are important residues for the interaction of the Mg2+ ion and eumelanin. Likewise, morphological changes based on different culture conditions (light/dark) showed that this protein is constitutive expressed and independent of blue light. The findings in this study demonstrate that pink chromoprotein is a melanosomal protein, and it possibly has a critical role in melanogenesis and the melanin polymerization. However, more experimental studies are needed to predict a possible mechanism of action and type of enzymatic activity.
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Affiliation(s)
- Mónica A Valdez-Solana
- Facultad de Ciencias Químicas GP,
Universidad Juárez del Estado de Durango, Gómez Palacio, México
| | - Erica K Ventura-García
- Facultad de Ciencias Químicas GP,
Universidad Juárez del Estado de Durango, Gómez Palacio, México
| | - Iván A Corral-Guerrero
- Facultad de Ciencias Químicas GP,
Universidad Juárez del Estado de Durango, Gómez Palacio, México
| | - Atahualpa Guzmán de Casa
- Departamento de Biotecnología y
Bioquímica, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato,
México
| | | | | | - Erick Sierra-Campos
- Facultad de Ciencias Químicas GP,
Universidad Juárez del Estado de Durango, Gómez Palacio, México,Erick Sierra-Campos, Facultad de Ciencias
Químicas GP, Universidad Juárez del Estado de Durango, Av. Artículo 123 S/N
Fracc, Filadelfia, Durango, Gómez Palacio C. P. 35015, México.
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Sadat A, Tiwari S, Sunidhi S, Chaphalkar A, Kochar M, Ali M, Zaidi Z, Sharma A, Verma K, Narayana Rao KB, Tripathi M, Ghosh A, Gautam D, Atul, Ray A, Mapa K, Chakraborty K. Conserved and divergent chaperoning effects of Hsp60/10 chaperonins on protein folding landscapes. Proc Natl Acad Sci U S A 2022; 119:e2118465119. [PMID: 35486698 PMCID: PMC9170145 DOI: 10.1073/pnas.2118465119] [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: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
The GroEL/ES chaperonin cavity surface charge properties, especially the negative charges, play an important role in its capacity to assist intracavity protein folding. Remarkably, the larger fraction of GroEL/ES negative charges are not conserved among different bacterial species, resulting in a large variation in negative-charge density in the GroEL/ES cavity across prokaryotes. Intriguingly, eukaryotic GroEL/ES homologs have the lowest negative-charge density in the chaperonin cavity. This prompted us to investigate if GroEL’s chaperoning mechanism changed during evolution. Using a model in vivo GroEL/ES substrate, we show that the ability of GroEL/ES to buffer entropic traps in the folding pathway of its substrate was partially dependent upon the negative-charge density inside its cavity. While this activity of GroEL/ES was found to be essential for Escherichia coli, it has been perfected in some organisms and diminished in others. However, irrespective of their charges, all the tested homologs retained their ability to regulate polypeptide chain collapse and remove enthalpic traps from folding pathways. The ability of these GroEL/ES homologs to buffer mutational variations in a model substrate correlated with their negative-charge density. Thus, Hsp60/10 chaperonins in different organisms may have changed to accommodate a different spectrum of mutations on their substrates.
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Affiliation(s)
- Anwar Sadat
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Satyam Tiwari
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - S. Sunidhi
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Aseem Chaphalkar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manisha Kochar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Mudassar Ali
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, India
| | - Zainab Zaidi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Akanksha Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kanika Verma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Kannan Boosi Narayana Rao
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Manjul Tripathi
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Asmita Ghosh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Deepika Gautam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Atul
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology–Delhi, New Delhi 110020, India
| | - Koyeli Mapa
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida 201314, India
| | - Kausik Chakraborty
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Chemical and System Biology Unit, CSIR–Institute of Genomics and Integrative Biology, New Delhi 110025, India
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