1
|
Vander Meersche Y, Cretin G, Gheeraert A, Gelly JC, Galochkina T. ATLAS: protein flexibility description from atomistic molecular dynamics simulations. Nucleic Acids Res 2024; 52:D384-D392. [PMID: 37986215 PMCID: PMC10767941 DOI: 10.1093/nar/gkad1084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/15/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.
Collapse
Affiliation(s)
- Yann Vander Meersche
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Gabriel Cretin
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Aria Gheeraert
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| |
Collapse
|
2
|
Das P, Majumder R, Sen N, Nandi SK, Ghosh A, Mandal M, Basak P. A computational analysis to evaluate deleterious SNPs of GSK3β, a multifunctional and regulatory protein, for metabolism, wound healing, and migratory processes. Int J Biol Macromol 2024; 256:128262. [PMID: 37989431 DOI: 10.1016/j.ijbiomac.2023.128262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023]
Abstract
This study focused on GSK-3β, a critical serine/threonine kinase with diverse cellular functions. However, there is limited understanding of the impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on its structure and function. Through an exhaustive in-silico investigation 12 harmful nsSNPs were predicted from a pool of 172 acquired from the NCBI dbSNP database using 12 established tools that detects deleterious SNPs. Consistently, these nsSNPs were discovered in locations with high levels of conservation. Notably, the three harmful nsSNPs F67C, A83T, and T138I were situated in the active/binding site of GSK-3β, which may affect the protein's capacity to bind to substrates and other proteins. Molecular dynamics simulations revealed that the F67C and T138I mutants had stable structures, indicating rigidness, whereas the A83T mutant was unstable. Analysis of secondary structures revealed different modifications in all mutant forms, which may affect the stability, functioning, and interactions of the protein. These mutations appear to alter the structural dynamics of GSK-3β, which may have functional ramifications, such as the formation of novel secondary structures and variations in coil-to-helix transitions. In conclusion, this study illuminates the possible structural and functional ramifications of these GSK-3 nsSNPs, revealing how protein compactness, stiffness, and interactions may affect biological activities.
Collapse
Affiliation(s)
- Pratik Das
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India
| | - Ranabir Majumder
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Nandita Sen
- Molecular biology wing, Dept of Biotechnology, PES University, Bangalore, India
| | - Samit Kumar Nandi
- Department of Veterinary Surgery & Radiology, West Bengal University of Animal and Fishery Sciences, Kolkata, India
| | - Arabinda Ghosh
- Department of Computational Biology and Biotechnology, Mahapurusha Srimanta Sankaradeva Viswavidyalaya, Guwahati Unit, Guwahati, Assam, India
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science & Technology, Indian Institute of Technology Kharagpur, India
| | - Piyali Basak
- School of Bioscience and Engineering, Jadavpur University, Kolkata, India.
| |
Collapse
|
3
|
Maulana H, Widyastuti Y, Herlina N, Hasbuna A, Al-Islahi ASH, Triratna L, Mayasari N. Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed. J Genet Eng Biotechnol 2023; 21:142. [PMID: 38008870 PMCID: PMC10678861 DOI: 10.1186/s43141-023-00600-y] [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: 07/20/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value. Aspergillus niger is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the phytase enzyme, as well as to determine the primer designs. METHOD This study used gene sequence data and protein-encoding phytase from Aspergillus niger that was collected manually from NCBI and PDB. The data was analyzed using SPDBV and then be aligned using the ClustalW Multiple Alignment features. The phylogenetic tree was built by Mega11 software. Primers were designed from selected candidate sequences that were analyzed. The designed primers were then simulated for PCR using FastPCR and SnapGene software. RESULTS There are 18 Aspergillus niger phytases in NCBI which is 14.87% of the total Aspergillus. There are 14 Aspergillus niger phytases that have identity above 95%. Aspergillus niger 110. M94550.1 is the closest strain to the PDB template. Candidate sources of phytase genes are Aspergillus niger 110.M94550.1, 48.2.BCMY01000003.1, and 92.JQ654450.1. The primer design has 2 possibilities of self-annealing and high melting temperature on the reverse primer. PCR simulation shows that the primer design can attach completely but still has the possibility of mispriming. CONCLUSION This study suggests promising results for the future development of phytase enzyme production from Aspergillus niger as a feed additive using genetic engineering to enhance the quality of livestock feed in Indonesia.
Collapse
Affiliation(s)
- Hamdan Maulana
- Faculty of Animal Husbandry, Department of Nutrition and Feed Technology, Universitas Padjadjaran, 45363, Jatinangor, Sumedang, West Java, Indonesia
| | - Yantyati Widyastuti
- National Research and Innovation Agency (BRIN), Research Center for Applied Microbiology, 16911, Cibinong, Bogor, West Java, Indonesia
| | - Nina Herlina
- National Research and Innovation Agency (BRIN), Research Center for Applied Microbiology, 16911, Cibinong, Bogor, West Java, Indonesia
| | - Abun Hasbuna
- Faculty of Animal Husbandry, Department of Nutrition and Feed Technology, Universitas Padjadjaran, 45363, Jatinangor, Sumedang, West Java, Indonesia
| | | | - Lita Triratna
- National Research and Innovation Agency (BRIN), Research Center for Applied Microbiology, 16911, Cibinong, Bogor, West Java, Indonesia
| | - Novi Mayasari
- Faculty of Animal Husbandry, Department of Nutrition and Feed Technology, Universitas Padjadjaran, 45363, Jatinangor, Sumedang, West Java, Indonesia.
| |
Collapse
|
4
|
Costa MGS, Batista PR, Gomes A, Bastos LS, Louet M, Floquet N, Bisch PM, Perahia D. MDexciteR: Enhanced Sampling Molecular Dynamics by Excited Normal Modes or Principal Components Obtained from Experiments. J Chem Theory Comput 2023; 19:412-425. [PMID: 36622950 DOI: 10.1021/acs.jctc.2c00599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal modes describing intrinsic collective motions. Herein, we developed a new automated open-source implementation, MDexciteR (https://github.com/mcosta27/MDexciteR), enabling the integration of MDeNM with two commonly used simulation programs with GPU support. Second, we generalized the method to include the excitation of principal components calculated from experimental ensembles. Finally, we evaluated whether the use of coarse-grained normal modes calculated with elastic network representations preserved the performance and accuracy of the method. The advantages and limitations of these new approaches are discussed based on results obtained for three different protein test cases: two globular and a protein/membrane system.
Collapse
Affiliation(s)
- Mauricio G S Costa
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113, CNRS, École Normale Supérieure Paris-Saclay, 4 Avenue des Sciences, 91190Gif-sur-Yvette, France
| | - Paulo R Batista
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
| | - Antoniel Gomes
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brasil
| | - Leonardo S Bastos
- Programa de Computação Científica, Vice-Presidência de Educação Informação e Comunicação, Fundação Oswaldo Cruz, Av. Brasil 4365, Residência Oficial, Manguinhos, 21040-900Rio de Janeiro, Brasil
| | - Maxime Louet
- Institut des Biomolecules Max Mousseron, UMR5247, CNRS, Université De Montpellier, ENSCM, 1919 Route de Mende, Montpellier, Cedex 0534095, France
| | - Nicolas Floquet
- Institut des Biomolecules Max Mousseron, UMR5247, CNRS, Université De Montpellier, ENSCM, 1919 Route de Mende, Montpellier, Cedex 0534095, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro21941-902, Brasil
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), UMR 8113, CNRS, École Normale Supérieure Paris-Saclay, 4 Avenue des Sciences, 91190Gif-sur-Yvette, France
| |
Collapse
|
5
|
Saeed AU, Rahman MU, Chen HF, Zheng J. Structural Insight of KSIII (β-Ketoacyl-ACP Synthase)-like Acyltransferase ChlB3 in the Biosynthesis of Chlorothricin. Molecules 2022; 27:molecules27196405. [PMID: 36234941 PMCID: PMC9573744 DOI: 10.3390/molecules27196405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/07/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Chlorothricin (CHL) belongs to a spirotetronate antibiotic family produced by Streptomyces antibioticus that inhibits pyruvate carboxylase and malate dehydrogenase. For the biosynthesis of CHL, ChlB3 plays a crucial role by introducing the 6-methylsalicylic acid (6MSA) moiety to ChlB2, an acyl carrier protein (ACP). However, the structural insight and catalytic mechanism of ChlB3 was unclear. In the current study, the crystal structure of ChlB3 was solved at 3.1 Å-resolution and a catalytic mechanism was proposed on the basis of conserved residues of structurally related enzymes. ChlB3 is a dimer having the same active sites as CerJ (a structural homologous enzyme) and uses a KSIII-like fold to work as an acyltransferase. The relaxed substrate specificity of ChlB3 was defined by its catalytic efficiencies (kcat/Km) for non-ACP tethered synthetic substrates such as 6MSA-SNAC, acetyl-SNAC, and cyclohexonyl-SNAC. ChlB3 successfully detached the 6MSA moiety from 6MSA-SNAC substrate and this hydrolytic activity demonstrated that ChlB3 has the potential to catalyze non-ACP tethered substrates. Structural comparison indicated that ChlB3 belongs to FabH family and showed 0.6–2.5 Å root mean square deviation (RMSD) with structural homologous enzymes. Molecular docking and dynamics simulations were implemented to understand substrate active site and structural behavior such as the open and closed conformation of the ChlB3 protein. The resultant catalytic and substrate recognition mechanism suggested that ChlB3 has the potential to use non-native substrates and minimize the labor of expressing ACP protein. This versatile acyltransferase activity may pave the way for manufacturing CHL variants and may help to hydrolyze several thioester-based compounds.
Collapse
Affiliation(s)
- Asad Ullah Saeed
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Jianting Zheng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence:
| |
Collapse
|
6
|
Dimić DS, Kaluđerović GN, Avdović EH, Milenković DA, Živanović MN, Potočňák I, Samoľová E, Dimitrijević MS, Saso L, Marković ZS, Dimitrić Marković JM. Synthesis, Crystallographic, Quantum Chemical, Antitumor, and Molecular Docking/Dynamic Studies of 4-Hydroxycoumarin-Neurotransmitter Derivatives. Int J Mol Sci 2022; 23:1001. [PMID: 35055194 PMCID: PMC8780855 DOI: 10.3390/ijms23021001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/20/2022] Open
Abstract
In this contribution, four new compounds synthesized from 4-hydroxycoumarin and tyramine/octopamine/norepinephrine/3-methoxytyramine are characterized spectroscopically (IR and NMR), chromatographically (UHPLC-DAD), and structurally at the B3LYP/6-311++G*(d,p) level of theory. The crystal structure of the 4-hydroxycoumarin-octopamine derivative was solved and used as a starting geometry for structural optimization. Along with the previously obtained 4-hydroxycoumarin-dopamine derivative, the intramolecular interactions governing the stability of these compounds were quantified by NBO and QTAIM analyses. Condensed Fukui functions and the HOMO-LUMO gap were calculated and correlated with the number and position of OH groups in the structures. In vitro cytotoxicity experiments were performed to elucidate the possible antitumor activity of the tested substances. For this purpose, four cell lines were selected, namely human colon cancer (HCT-116), human adenocarcinoma (HeLa), human breast cancer (MDA-MB-231), and healthy human lung fibroblast (MRC-5) lines. A significant selectivity towards colorectal carcinoma cells was observed. Molecular docking and molecular dynamics studies with carbonic anhydrase, a prognostic factor in several cancers, complemented the experimental results. The calculated MD binding energies coincided well with the experimental activity, and indicated 4-hydroxycoumarin-dopamine and 4-hydroxycoumarin-3-methoxytyramine as the most active compounds. The ecotoxicology assessment proved that the obtained compounds have a low impact on the daphnia, fish, and green algae population.
Collapse
Affiliation(s)
- Dušan S. Dimić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia;
| | - Goran N. Kaluđerović
- Department of Engineering and Natural Sciences, University of Applied Sciences Merseburg, Eberhard-Leibnitz-Straße 2, DE-06217 Merseburg, Germany;
| | - Edina H. Avdović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (E.H.A.); (D.A.M.); (M.N.Ž.); (Z.S.M.)
| | - Dejan A. Milenković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (E.H.A.); (D.A.M.); (M.N.Ž.); (Z.S.M.)
| | - Marko N. Živanović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (E.H.A.); (D.A.M.); (M.N.Ž.); (Z.S.M.)
| | - Ivan Potočňák
- Institute of Chemistry, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovakia;
| | - Erika Samoľová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic;
| | - Milena S. Dimitrijević
- Department of Life Sciences, Institute for Multidisciplinary Research, University of Belgrade, Kneza Višeslava 1, 11030 Belgrade, Serbia;
| | - Luciano Saso
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - Zoran S. Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (E.H.A.); (D.A.M.); (M.N.Ž.); (Z.S.M.)
| | | |
Collapse
|
7
|
Šterk M, Markovič R, Marhl M, Fajmut A, Dobovišek A. Response to "Comments on the paper 'Flexibility of enzymatic transitions as a hallmark of optimized enzyme steady-state kinetics and thermodynamics'". Comput Biol Chem 2021; 95:107572. [PMID: 34531143 DOI: 10.1016/j.compbiolchem.2021.107572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marko Šterk
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Rene Markovič
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Energy Technology, Hočevarjev trg 1, 8270 Krško, Slovenia
| | - Marko Marhl
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska ulica 8, 2000 Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška cesta 160, 2000 Maribor, Slovenia
| | - Aleš Fajmut
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Health Sciences, Žitna ulica 15, 2000 Maribor, Slovenia
| | - Andrej Dobovišek
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška cesta 160, 2000 Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska ulica 8, 2000 Maribor, Slovenia.
| |
Collapse
|
8
|
Jovanović JĐ, Antonijević M, El‐Emam AA, Marković Z. Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M pro. ChemistrySelect 2021; 6:8603-8610. [PMID: 34909459 PMCID: PMC8662094 DOI: 10.1002/slct.202101898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022]
Abstract
In this study, the inhibitory potency of four adamantly- isothiourea derivatives (compounds 1 [4-bromobenzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 2 [3,5-bis(trifluoromethyl)benzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 3 [4-bromobenzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate] and 4 [3,5-bis(trifluoromethyl)benzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate]) was evaluated against SARS-CoV-2 targeted proteins. The investigated compounds 1-4 possess a similar structure to opaganib, which is used in studies like a potential drug for COVID-19 treatment. Since examined adamantly-isothiourea derivatives (1-4) shown broad-spectrum of antibacterial activity and significant in vitro cytotoxic effects against five human tumor cell lines and shown similarity in structure with opaganib, it was of interest to study their inhibitory potency toward some SARS-CoV-2 proteins such as SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G. The inhibitory potency of studied compounds is examined using molecular docking and molecular dynamic simulations. The results of molecular docking simulations indicate compound 1 as the most prominent candidate of inhibition of SARS-CoV-2 main protease Mpro (▵Gbind=11.24 kcal/mol), while almost the same inhibition potency of all studied compounds is exhibited toward D614G. Regarding the results obtained by molecular dynamic simulations, compounds 1 and 4 possess similar inhibitory potency toward SARS-CoV-2 main protease Mpro as opaganib (▵Gbind ≈ 40 kcal/mol).
Collapse
Affiliation(s)
- Jelena Đorović Jovanović
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Marko Antonijević
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Ali A. El‐Emam
- Department of Medicinal ChemistryFaculty of PharmacyMansoura UniversityMansoura35516Egypt
| | - Zoran Marković
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| |
Collapse
|
9
|
Kisten K, Kumalo HM, Machaba KE, Ndagi U, Mhlongo NN. Drug repurposing approach against Mycobacterium tuberculosis Enoyl-[acyl-carrier-protein] reductase: insight from molecular dynamics simulations. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1968390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Kimona Kisten
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M. Kumalo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kgothatso E. Machaba
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Ndumiso N. Mhlongo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
10
|
Fields PA. Reductionism in the study of enzyme adaptation. Comp Biochem Physiol B Biochem Mol Biol 2021; 254:110574. [PMID: 33600949 DOI: 10.1016/j.cbpb.2021.110574] [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: 01/07/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
One of the principal goals of comparative biology is the elucidation of mechanisms by which organisms adapt to different environments. The study of enzyme structure, function, and stability has contributed significantly to this effort, by revealing adaptation at a molecular level. Comparative biochemistry, including enzymology, necessarily pursues a reductionist approach in describing the function and structure of biomolecules, allowing more straightforward study of molecular systems by removing much of the complexity of their biological milieu. Although this reductionism has allowed a remarkable series of discoveries linking chemical processes to metabolism and to whole-organism function in the context of the environment, it also has the potential to mislead when careful consideration is not made of the simplifying assumptions inherent to such research. In this review, a brief history of the growth of enzymology, its reliance on a reductionist philosophy, and its contributions to our understanding of biological systems is given. Examples then are provided of research techniques, based on a reductionist approach, that have advanced our knowledge about enzyme adaptation to environmental stresses, including stability assays, enzyme kinetics, and the impact of solute composition on enzyme function. In each case, the benefits of the reductionist nature of the approach is emphasized, notable advances are described, but potential drawbacks due to inherent oversimplification of the study system are also identified.
Collapse
Affiliation(s)
- Peter A Fields
- Biology Department, Franklin & Marshall College, Lancaster, PA 17603, USA.
| |
Collapse
|
11
|
Šterk M, Markovič R, Marhl M, Fajmut A, Dobovišek A. Flexibility of enzymatic transitions as a hallmark of optimized enzyme steady-state kinetics and thermodynamics. Comput Biol Chem 2021; 91:107449. [PMID: 33588154 DOI: 10.1016/j.compbiolchem.2021.107449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 09/05/2020] [Accepted: 02/02/2021] [Indexed: 11/25/2022]
Abstract
We investigate the relations between the enzyme kinetic flexibility, the rate of entropy production, and the Shannon information entropy in a steady-state enzyme reaction. All these quantities are maximized with respect to enzyme rate constants. We show that the steady-state, which is characterized by the most flexible enzymatic transitions between the enzyme conformational states, coincides with the global maxima of the Shannon information entropy and the rate of entropy production. This steady-state of an enzyme is referred to as globally optimal. This theoretical approach is then used for the analysis of the kinetic and the thermodynamic performance of the enzyme triose-phosphate isomerase. The analysis reveals that there exist well-defined maxima of the kinetic flexibility, the rate of entropy production, and the Shannon information entropy with respect to any arbitrarily chosen rate constant of the enzyme and that these maxima, calculated from the measured kinetic rate constants for the triose-phosphate isomerase are lower, however of the same order of magnitude, as the maxima of the globally optimal state of the enzyme. This suggests that the triose-phosphate isomerase could be a well, but not fully evolved enzyme, as it was previously claimed. Herein presented theoretical investigations also provide clear evidence that the flexibility of enzymatic transitions between the enzyme conformational states is a requirement for the maximal Shannon information entropy and the maximal rate of entropy production.
Collapse
Affiliation(s)
- Marko Šterk
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 8, 2000, Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška Cesta 160, 2000, Maribor, Slovenia
| | - Rene Markovič
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Energy Technology, Hočevarjev Trg 1, 8270, Krško, Slovenia
| | - Marko Marhl
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 8, 2000, Maribor, Slovenia; University of Maribor, Faculty of Education, Koroška Cesta 160, 2000, Maribor, Slovenia
| | - Aleš Fajmut
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Health Sciences, Žitna Ulica 15, 2000, Maribor, Slovenia
| | - Andrej Dobovišek
- University of Maribor, Faculty of Natural Sciences and Mathematics, Koroška Cesta 160, 2000, Maribor, Slovenia; University of Maribor, Faculty of Medicine, Taborska Ulica 8, 2000, Maribor, Slovenia.
| |
Collapse
|
12
|
Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
Collapse
Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
| |
Collapse
|
13
|
Olanlokun JO, Olotu FA, Idowu OT, Agoni C, David MO, Soliman M, Olorunsogo OO. In vitro, in silico studies of newly isolated tetrahydro-4-(7-hydroxy-10-methoxy-6, 14-dimethyl-15-m-tolylpentadec-13-enyl) pyran-2-one and isobutyryl acetate compounds from Alstonia boonei stem bark. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
14
|
Cornell RB. Membrane Lipids Assist Catalysis by CTP: Phosphocholine Cytidylyltransferase. J Mol Biol 2020; 432:5023-5042. [PMID: 32234309 DOI: 10.1016/j.jmb.2020.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
While most of the articles in this issue review the workings of integral membrane enzymes, in this review, we describe the catalytic mechanism of an enzyme that contains a soluble catalytic domain but appears to catalyze its reaction on the membrane surface, anchored and assisted by a separate regulatory amphipathic helical domain and inter-domain linker. Membrane partitioning of CTP: phosphocholine cytidylyltransferase (CCT), a key regulatory enzyme of phosphatidylcholine metabolism, is regulated chiefly by changes in membrane phospholipid composition, and boosts the enzyme's catalytic efficiency >200-fold. Catalytic enhancement by membrane binding involves the displacement of an auto-inhibitory helix from the active site entrance-way and promotion of a new conformational ensemble for the inter-domain, allosteric linker that has an active role in the catalytic cycle. We describe the evidence for close contact between membrane lipid, a compact allosteric linker, and the CCT active site, and discuss potential ways that this interaction enhances catalysis.
Collapse
Affiliation(s)
- Rosemary B Cornell
- Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada V5A-1S6.
| |
Collapse
|
15
|
Yang LQ, Yin YR, Shen JX, Li Y, Liu SQ, Sang P. Insight derived from molecular dynamics simulation into cold-adaptation mechanism of trypsins. J Biomol Struct Dyn 2020; 38:2768-2776. [DOI: 10.1080/07391102.2019.1635529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, P. R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, P.R. China
| | - Yi-Rui Yin
- College of Agriculture and Biological Science, Dali University, Dali, P. R. China
| | - Jian-Xin Shen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, P.R. China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, P. R. China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali University, Dali, P.R. China
| |
Collapse
|
16
|
Lambrughi M, Sanader Maršić Ž, Saez-Jimenez V, Mapelli V, Olsson L, Papaleo E. Conformational gating in ammonia lyases. Biochim Biophys Acta Gen Subj 2020; 1864:129605. [PMID: 32222547 DOI: 10.1016/j.bbagen.2020.129605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Ammonia lyases are enzymes of industrial and biomedical interest. Knowledge of structure-dynamics-function relationship in ammonia lyases is instrumental for exploiting the potential of these enzymes in industrial or biomedical applications. METHODS We investigated the conformational changes in the proximity of the catalytic pocket of a 3-methylaspartate ammonia lyase (MAL) as a model system. At this scope, we used microsecond all-atom molecular dynamics simulations, analyzed with dimensionality reduction techniques, as well as in terms of contact networks and correlated motions. RESULTS We identify two regulatory elements in the MAL structure, i.e., the β5-α2 loop and the helix-hairpin-loop subdomain. These regulatory elements undergo conformational changes switching from 'occluded' to 'open' states. The rearrangements are coupled to changes in the accessibility of the active site. The β5-α2 loop and the helix-hairpin-loop subdomain modulate the formation of tunnels from the protein surface to the catalytic site, making the active site more accessible to the substrate when they are in an open state. CONCLUSIONS Our work pinpoints a sequential mechanism, in which the helix-hairpin-loop subdomain of MAL needs to break a subset of intramolecular interactions first to favor the displacement of the β5-α2 loop. The coupled conformational changes of these two elements contribute to modulate the accessibility of the catalytic site. GENERAL SIGNIFICANCE Similar molecular mechanisms can have broad relevance in other ammonia lyases with similar regulatory loops. Our results also imply that it is important to account for protein dynamics in the design of variants of ammonia lyases for industrial and biomedical applications.
Collapse
Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Željka Sanader Maršić
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Veronica Saez-Jimenez
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Valeria Mapelli
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Lisbeth Olsson
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark; Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
17
|
Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, Maisey K, Yáñez JM, Valenzuela H, Cea PA, Castro-Fernandez V, Tort L, Sandino AM, Imarai M, Reyes-López FE. Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon ( Salmo salar). Front Genet 2020; 10:1406. [PMID: 32174954 PMCID: PMC7056891 DOI: 10.3389/fgene.2019.01406] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ccl19], integrin β2 (itβ2, also named cd18), glutathione transferase omega-1 [gsto-1], heat shock 70 KDa protein [hsp70], major histocompatibility complex class I [mhc-I]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5’-untranslated region (UTR) or 3’-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU) showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2 c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs) may be associated to differences in the local rate of elongation. Nonsynonymous SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology modeling to predict the effect of these nonsynonymous SNPs, the most relevant nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T > C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1 variants have significant differences in their conformational dynamics, suggesting these SNPs could have allosteric effects modulating its catalysis. Altogether, these results suggest that candidate SNPs identified may play a crucial potential role in the immune response of Atlantic salmon.
Collapse
Affiliation(s)
- Eva Vallejos-Vidal
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Jaime Andrés Rivas-Pardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Kevin Maisey
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Hector Valenzuela
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Pablo A Cea
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Lluis Tort
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana M Sandino
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E Reyes-López
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
18
|
Simonis H, Yaghootfam C, Sylvester M, Gieselmann V, Matzner U. Evolutionary redesign of the lysosomal enzyme arylsulfatase A increases efficacy of enzyme replacement therapy for metachromatic leukodystrophy. Hum Mol Genet 2020; 28:1810-1821. [PMID: 30657900 DOI: 10.1093/hmg/ddz020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Protein engineering is a means to optimize protein therapeutics developed for the treatment of so far incurable diseases including cancers and genetic disorders. Here we report on an engineering approach in which we successfully increased the catalytic rate constant of an enzyme that is presently evaluated in enzyme replacement therapies (ERT) of a lysosomal storage disease (LSD). Although ERT is a treatment option for many LSDs, outcomes are lagging far behind expectations for most of them. This has been ascribed to insufficient enzyme activities accumulating in tissues difficult to target such as brain and peripheral nerves. We show for human arylsulfatase A (hARSA) that the activity of a therapeutic enzyme can be substantially increased by reversing activity-diminishing and by inserting activity-promoting amino acid substitutions that had occurred in the evolution of hominids and non-human mammals, respectively. The potential of this approach, here designated as evolutionary redesign, was highlighted by the observation that murinization of only 1 or 3 amino acid positions increased the hARSA activity 3- and 5-fold, with little impact on stability, respectively. The two kinetically optimized hARSA variants showed no immunogenic potential in ERT of a humanized ARSA knockout mouse model of metachromatic leukodystrophy (MLD) and reduced lysosomal storage of kidney, peripheral and central nervous system up to 3-fold more efficiently than wild-type hARSA. Due to their safety profile and higher therapeutic potential the engineered hARSA variants might represent major advances for future enzyme-based therapies of MLD and stimulate analogous approaches for other enzyme therapeutics.
Collapse
Affiliation(s)
- Heidi Simonis
- Institute of Biochemistry and Molecular Biology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Claudia Yaghootfam
- Institute of Biochemistry and Molecular Biology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Marc Sylvester
- Institute of Biochemistry and Molecular Biology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Volkmar Gieselmann
- Institute of Biochemistry and Molecular Biology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Ulrich Matzner
- Institute of Biochemistry and Molecular Biology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| |
Collapse
|
19
|
Sang P, Tian SH, Meng ZH, Yang LQ. Anti-HIV drug repurposing against SARS-CoV-2. RSC Adv 2020; 10:15775-15783. [PMID: 35493667 PMCID: PMC9052367 DOI: 10.1039/d0ra01899f] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/01/2020] [Indexed: 12/14/2022] Open
Abstract
A novel severe acute respiratory syndrome human coronavirus (SARS HCoV) was identified from respiratory illness patients (named SARS-CoV-2 by ICTV) in December 2019 and has recently emerged as a serious threat to world public health. However, no approved drugs have been found to effectively inhibit the virus. Since it has been reported that HIV protease inhibitors can be used as anti-SARS drugs by targeting SARS-CoV-1 3CLpro, we chose six approved anti-HIV drugs and investigated their binding interactions with 3CLpro to evaluate their potential to become clinical drugs for the new coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection. The molecular docking results indicate that the 3CLpro of SARS-CoV-2 has a higher binding affinity for all the studied inhibitors than does SARS-CoV-1. Two docking complexes (indinavir and darunavir) with high docking scores were further subjected to MM-PBSA binding free energy calculations to detail the molecular interactions between these two protease inhibitors and SARS HCoV 3CLpro. Our results show that, among the inhibitors tested, darunavir has the highest binding affinity with SARS-CoV-2 and SARS-CoV-1 3CLpro, indicating that it may have the potential to be used as an anti-COVID-19 clinical drug. The mechanism behind the increased binding affinity of HIV protease inhibitors toward SARS-CoV-2 3CLpro (as compared to SARS-CoV-1) was investigated by MD simulations. Our study provides insight into the possible role of structural flexibility during interactions between SARS HCoV 3CLpro and inhibitors and sheds light on structure-based design of anti-COVID-19 drugs targeting SARS-CoV-2 3CLpro. A novel severe acute respiratory syndrome human coronavirus (SARS HCoV) was identified from respiratory illness patients (named SARS-CoV-2 by ICTV) in December 2019 and has recently emerged as a serious threat to world public health.![]()
Collapse
Affiliation(s)
- Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Shu-Hui Tian
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Zhao-Hui Meng
- NHC Key Laboratory of Drug Addiction Medicine
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| |
Collapse
|
20
|
Su HH, Peng F, Xu P, Wu XL, Zong MH, Yang JG, Lou WY. Enhancing the thermostability and activity of uronate dehydrogenase from Agrobacterium tumefaciens LBA4404 by semi-rational engineering. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-019-0267-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Glucaric acid, one of the aldaric acids, has been declared a “top value-added chemical from biomass”, and is especially important in the food and pharmaceutical industries. Biocatalytic production of glucaric acid from glucuronic acid is more environmentally friendly, efficient and economical than chemical synthesis. Uronate dehydrogenases (UDHs) are the key enzymes for the preparation of glucaric acid in this way, but the poor thermostability and low activity of UDH limit its industrial application. Therefore, improving the thermostability and activity of UDH, for example by semi-rational design, is a major research goal.
Results
In the present work, three UDHs were obtained from different Agrobacterium tumefaciens strains. The three UDHs have an approximate molecular weight of 32 kDa and all contain typically conserved UDH motifs. All three UDHs showed optimal activity within a pH range of 6.0–8.5 and at a temperature of 30 °C, but the UDH from A. tumefaciens (At) LBA4404 had a better catalytic efficiency than the other two UDHs (800 vs 600 and 530 s−1 mM−1). To further boost the catalytic performance of the UDH from AtLBA4404, site-directed mutagenesis based on semi-rational design was carried out. An A39P/H99Y/H234K triple mutant showed a 400-fold improvement in half-life at 59 °C, a 5 °C improvement in $$ {\text{T}}_{ 5 0}^{ 1 0} $$
T
50
10
value and a 2.5-fold improvement in specific activity at 30 °C compared to wild-type UDH.
Conclusions
In this study, we successfully obtained a triple mutant (A39P/H99Y/H234K) with simultaneously enhanced activity and thermostability, which provides a novel alternative for the industrial production of glucaric acid from glucuronic acid.
Collapse
|
21
|
A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states. J Math Biol 2019; 79:631-672. [PMID: 31030299 PMCID: PMC9841320 DOI: 10.1007/s00285-019-01372-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 12/16/2018] [Indexed: 01/18/2023]
Abstract
Calculations of electrostatic potential and solvation free energy of macromolecules are essential for understanding the mechanism of many biological processes. In the classical implicit solvent Poisson-Boltzmann (PB) model, the macromolecule and water are modeled as two-dielectric media with a sharp border. However, the dielectric property of interior cavities and ion-channels is difficult to model realistically in a two-dielectric setting. In fact, the detection of water molecules in a protein cavity remains to be an experimental challenge. This introduces an uncertainty, which affects the subsequent solvation free energy calculation. In order to compensate this uncertainty, a novel super-Gaussian dielectric PB model is introduced in this work, which devices an inhomogeneous dielectric distribution to represent the compactness of atoms and characterizes empty cavities via a gap dielectric value. Moreover, the minimal molecular surface level set function is adopted so that the dielectric profile remains to be smooth when the protein is transferred from water phase to vacuum. An important feature of this new model is that as the order of super-Gaussian function approaches the infinity, the dielectric distribution reduces to a piecewise constant of the two-dielectric model. Mathematically, an effective dielectric constant analysis is introduced in this work to benchmark the dielectric model and select optimal parameter values. Computationally, a pseudo-time alternative direction implicit (ADI) algorithm is utilized for solving the super-Gaussian PB equation, which is found to be unconditionally stable in a smooth dielectric setting. Solvation free energy calculation of a Kirkwood sphere and various proteins is carried out to validate the super-Gaussian model and ADI algorithm. One macromolecule with both water filled and empty cavities is employed to demonstrate how the cavity uncertainty in protein structure can be bypassed through dielectric modeling in biomolecular electrostatic analysis.
Collapse
|
22
|
Liao H, Gong JY, Yang Y, Jiang ZD, Zhu YB, Li LJ, Ni H, Li QB. Enhancement of the thermostability of Aspergillus niger α-l-rhamnosidase based on PoPMuSiC algorithm. J Food Biochem 2019; 43:e12945. [PMID: 31368575 DOI: 10.1111/jfbc.12945] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/24/2019] [Indexed: 11/27/2022]
Abstract
α-l-Rhamnosidase is a biotechnologically important enzyme in food industry and in the preparation of drugs and drug precursors. To expand the functionality of our previously cloned α-l-rhamnosidase from Aspergillus niger JMU-TS528, 14 mutants were constructed based on the changes of the folding free energy (ΔΔG), predicted by the PoPMuSiC algorithm. Among them, six single-site mutants displayed higher thermal stability than wild type (WT). The combinational mutant K573V-E631F displayed even higher thermostability than six single-site mutants. The spectra analyses displayed that the WT and K573V-E631F had almost similar secondary and tertiary structure profiles. The simulated protein structure-based interaction analysis and molecular dynamics calculation were further implemented to assess the conformational preferences of the K573V-E631F. The improved thermostability of mutant K573V-E631F may be attributed to the introduction of new cation-π and hydrophobic interactions, and the overall improvement of the enzyme conformation. PRACTICAL APPLICATIONS: The stability of enzymes, particularly with regards to thermal stability remains a critical issue in industrial biotechnology and industrial processing generally tends to higher ambient temperature to inhibit microbial growth. Most of the α-l-rhamnosidases are usually active at temperature from 30 to 60°C, which are apt to denature at temperatures over 60°C. To expand the functionality of our previously cloned α-l-rhamnosidase from Aspergillus niger JMU-TS528, we used protein engineering methods to increase the thermal stability of the α-l-rhamnosidase. Practically, conducting reactions at high temperatures enhances the solubility of substrates and products, increases the reaction rate thus reducing the reaction time, and inhibits the growth of contaminating microorganisms. Thus, the improvement on the thermostability of α-l-rhamnosidase on the one hand can increase enzyme efficacy; on the other hand, the high ambient temperature would enhance the solubility of natural substrates of α-l-rhamnosidase, such as naringin, rutin, and hesperidin, which are poorly dissolved in water at room temperature. Protein thermal resistance is an important issue beyond its obvious industrial importance. The current study also helps in the structure-function relationship study of α-l-rhamnosidase.
Collapse
Affiliation(s)
- Hui Liao
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Jian-Ye Gong
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yan Yang
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Ze-Dong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Yan-Bing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| | - Li-Jun Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen, China.,Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, China.,Research Center of Food Biotechnology of Xiamen City, Xiamen, China
| | - Qing-Biao Li
- College of Food and Biological Engineering, Jimei University, Xiamen, China
| |
Collapse
|
23
|
|
24
|
Cold survival strategies for bacteria, recent advancement and potential industrial applications. Arch Microbiol 2018; 201:1-16. [PMID: 30478730 DOI: 10.1007/s00203-018-1602-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/04/2018] [Accepted: 11/24/2018] [Indexed: 12/12/2022]
Abstract
Microorganisms have evolved themselves to thrive under various extreme environmental conditions such as extremely high or low temperature, alkalinity, and salinity. These microorganisms adapted several metabolic processes to survive and reproduce efficiently under such extreme environments. As the major proportion of earth is covered with the cold environment and is exploited by human beings, these sites are not pristine anymore. Human interventions are a great reason for disturbing the natural biogeochemical cycles in these regions. The survival strategies of these organisms have shown great potential for helping us to restore these pristine sites and the use of isolated cold-adapted enzymes from these organisms has also revolutionized various industrial products. This review gives you the insight of psychrophilic enzyme adaptations and their industrial applications.
Collapse
|
25
|
Wu X, Fraser K, Zha J, Dordick JS. Flexible Peptide Linkers Enhance the Antimicrobial Activity of Surface-Immobilized Bacteriolytic Enzymes. ACS APPLIED MATERIALS & INTERFACES 2018; 10:36746-36756. [PMID: 30281274 DOI: 10.1021/acsami.8b14411] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Chemical linkers are frequently used in enzyme immobilization to improve enzyme flexibility and activity, whereas peptide linkers, although ubiquitous in protein engineering, are much less explored in enzyme immobilization. Here, we report peptide-linker-assisted noncovalent immobilization of the bacteriolytic enzyme lysostaphin (Lst) to generate anti- Staphylococcus aureus surfaces. Lst was immobilized through affinity tags onto a silica surface (glass slides) and nickel nitrilotriacetic acid (NiNTA) agarose beads via silica-binding peptides (SiBPs) or a hexahistidine tag (His-tag) fused at the C-terminus of Lst, respectively. By inserting specific peptide linkers upstream of the SiBP or His-tag, the immobilized enzymes killed >99.5% of S. aureus ATCC 6538 cells (108 CFU/mL) within 3 h in buffer and could be reused multiple times without significant loss of activity. In contrast, immobilized Lst without a peptide linker was less active/stable. Molecular modeling of Lst-linker-affinity tag constructs illustrated that the presence of the peptide linkers enhanced the molecular flexibility of the proximal Lst binding domain, which interacts with the bacterial substrate, and such increased flexibility correlated with increased antimicrobial activity. We further show that Lst immobilized onto NiNTA beads retained the ability to kill ∼99% of a 108 CFU/mL microbial challenge even in the presence of 1% of a commercial anionic surfactant, C12-14 alcohol EO 3:1 sodium sulfate, when the Lst construct contained a decapeptide linker containing glycine, serine, and alanine residues. This linker-assisted immobilization strategy could be extended to an unrelated lytic enzyme, the endolysin PlyPH, to target Bacillus anthracis Sterne cells either in buffer or in the presence of anionic surfactants. Our approach, therefore, provides a facile route to the use of antimicrobial enzymes on surfaces.
Collapse
|
26
|
Abdullahi M, Olotu FA, Soliman ME. Solving the riddle: Unraveling the mechanisms of blocking the binding of leukotoxin by therapeutic antagonists in periodontal diseases. J Cell Biochem 2018; 119:9364-9379. [PMID: 30129224 DOI: 10.1002/jcb.27254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022]
Abstract
Aggregatibacter actinomycetemcomitans is a Gram-negative bacteria that has gained wide recognition for its causative role in the development of various immune diseases, which includes localized aggressive periodontitis. Its ability to evade host defense mechanisms is mediated by the secretion of leukotoxin (LtxA), which induces death of white blood cells (leukocytes) by specific binding to their surface-expressed leukocyte function-associated receptor (LFA-1) in its active state. Therapeutic compounds that interfere with this pathogenic process and abrogate A. actinomycetemcomitans virulence have been reported in literature. These include doxycycline, and more recently phytochemical compounds such as hamamelitanin, resveratrol, naringin, and quercetin. However, the question remains how do they work? Therefore, with the aid of computational tools, we explore the molecular mechanisms by which they possibly elicit their therapeutic functions. Molecular mechanics Poisson/Boltzmann surface area analyses revealed that these compounds bind favorably to active LFA-1 with high affinity and considerable stability, indicative of their ability to occupy the LtxA binding site (LBS) and prevent LtxA binding. The conformational transition of open LFA-1 to its closed state further describe the mechanistic activity of these compounds. In addition to notable reductions in structural mobility and flexibility, the burial of surface-exposed interactive side chains at the LBS was observed, an occurrence that could alter the complementary binding of LtxA. It is also important to mention that these occurrences were induced more prominently by the phytochemicals. We believe that these findings will enhance the scope of drug design and discovery for potent LtxA antagonists with improved activities and therapeutic efficacies in the treatment of virulent A. actinomycetemcomitans diseases.
Collapse
Affiliation(s)
- Maryam Abdullahi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
27
|
Hu R, Rodrigues JV, Pradeep Waduge J, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. ACS NANO 2018; 12:4494-4502. [PMID: 29630824 PMCID: PMC9016714 DOI: 10.1021/acsnano.8b00734] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.
Collapse
Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - João V. Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J Pradeep Waduge
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hirohito Yamazaki
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yasmin Chishti
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
- Corresponding Authors:.,
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Authors:.,
| |
Collapse
|
28
|
Correa L, Borguesan B, Farfan C, Inostroza-Ponta M, Dorn M. A Memetic Algorithm for 3-D Protein Structure Prediction Problem. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:690-704. [PMID: 27925594 DOI: 10.1109/tcbb.2016.2635143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Memetic Algorithms are population-based metaheuristics intrinsically concerned with exploiting all available knowledge about the problem under study. The incorporation of problem domain knowledge is not an optional mechanism, but a fundamental feature of the Memetic Algorithms. In this paper, we present a Memetic Algorithm to tackle the three-dimensional protein structure prediction problem. The method uses a structured population and incorporates a Simulated Annealing algorithm as a local search strategy, as well as ad-hoc crossover and mutation operators to deal with the problem. It takes advantage of structural knowledge stored in the Protein Data Bank, by using an Angle Probability List that helps to reduce the search space and to guide the search strategy. The proposed algorithm was tested on nineteen protein sequences of amino acid residues, and the results show the ability of the algorithm to find native-like protein structures. Experimental results have revealed that the proposed algorithm can find good solutions regarding root-mean-square deviation and global distance total score test in comparison with the experimental protein structures. We also show that our results are comparable in terms of folding organization with state-of-the-art prediction methods, corroborating the effectiveness of our proposal.
Collapse
|
29
|
Gustafsson C, Vassiliev S, Kürten C, Syrén PO, Brinck T. MD Simulations Reveal Complex Water Paths in Squalene-Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site. ACS OMEGA 2017; 2:8495-8506. [PMID: 31457386 PMCID: PMC6645472 DOI: 10.1021/acsomega.7b01084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 06/10/2023]
Abstract
Squalene-hopene cyclase catalyzes the cyclization of squalene to hopanoids. A previous study has identified a network of tunnels in the protein, where water molecules have been indicated to move. Blocking these tunnels by site-directed mutagenesis was found to change the activation entropy of the catalytic reaction from positive to negative with a concomitant lowering of the activation enthalpy. As a consequence, some variants are faster and others are slower than the wild type (wt) in vitro under optimal reaction conditions for the wt. In this study, molecular dynamics (MD) simulations have been performed for the wt and the variants to investigate how the mutations affect the protein structure and the water flow in the enzyme, hypothetically influencing the activation parameters. Interestingly, the tunnel-obstructing variants are associated with an increased flow of water in the active site, particularly close to the catalytic residue Asp376. MD simulations with the substrate present in the active site indicate that the distance for the rate-determining proton transfer between Asp376 and the substrate is longer in the tunnel-obstructing protein variants than in the wt. On the basis of the previous experimental results and the current MD results, we propose that the tunnel-obstructing variants, at least partly, could operate by a different catalytic mechanism, where the proton transfer may have contributions from a Grotthuss-like mechanism.
Collapse
Affiliation(s)
- Camilla Gustafsson
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
| | - Serguei Vassiliev
- Department
of Biological Sciences, Brock University, Mackenzie Chown F 234, 1812 Sir
Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Charlotte Kürten
- Science
for Life Laboratory, Stockholm—School of Biotechnology, Division
of Proteomics and Nanobiotechnology, KTH
Royal Institute of Technology, Tomtebodavägen 23a, 171 65 Solna, Sweden
| | - Per-Olof Syrén
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
- Science
for Life Laboratory, Stockholm—School of Biotechnology, Division
of Proteomics and Nanobiotechnology, KTH
Royal Institute of Technology, Tomtebodavägen 23a, 171 65 Solna, Sweden
| | - Tore Brinck
- Applied
Physical Chemistry, School of Chemical Science and Engineering, KTH Royal Institute of Technology, Teknikringen 36, 100 44 Stockholm, Sweden
| |
Collapse
|
30
|
Prasad S, Roy I. Obtaining a high activity subtilisin preparation by controlled thermal stress in n-octane. Anal Biochem 2017; 534:86-90. [PMID: 28732585 DOI: 10.1016/j.ab.2017.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/10/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
The use of enzymes in organic solvents has considerably widened their repertoire of applications. Such low water containing media also offer the possibility of carrying out enzymatic reactions at higher temperatures and enhancing reaction yields. The utility of such preparations is limited by the damage caused to the protein structure during freeze-drying. This work investigates the result of exposing the proteolytic enzyme subtilisin to high temperature in low water containing n-octane on its activity in aqueous and non-aqueous media. Exposing subtilisin at 90 °C for 5 h led to 18-fold improvement in its transesterification activity even at the normal assay temperature (37 °C) when compared with the untreated enzyme. The use of n-octane as the reaction medium was important as it helped to retain the three-dimensional architecture of the enzyme and should be considered while designing strategies for obtaining high activity preparations of other enzymes. Structural analysis using differential scanning fluorimetry showed that the enzyme lost its structure after heating in aqueous medium but retained it when heated in organic solvent. The simplicity and general applicability of the strategy should make it useful for obtaining highly active preparations of other enzymes as well.
Collapse
Affiliation(s)
- Shivcharan Prasad
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India.
| |
Collapse
|
31
|
Sang P, Hu W, Ye YJ, Li LH, Zhang C, Xie YH, Meng ZH. In silico screening, molecular docking, and molecular dynamics studies of SNP-derived human P5CR mutants. J Biomol Struct Dyn 2017; 35:2441-2453. [PMID: 27677826 DOI: 10.1080/07391102.2016.1222967] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/07/2016] [Indexed: 01/13/2023]
Abstract
Pyrroline-5-carboxylate reductase (P5CR) encoded by PYCR1 gene is a housekeeping enzyme that catalyzes the reduction of P5C to proline using NAD(P)H as the cofactor. In this study, we used in silico approaches to examine the role of nonsynonymous single-nucleotide polymorphisms in the PYCR1 gene and their putative functions in the pathogenesis of Cutis Laxa. Among the 348 identified SNPs, 15 were predicted to be potentially damaging by both SIFT and PolyPhen tools; of them two SNP-derived mutations, R119G and G206W, have been previously reported to correlate with Cutis Laxa. These two mutations were therefore selected to be mapped to the wild-type (WT) P5CR structure for further structural and functional analyses. The results of comparative computational analyses using I-Mutant and Autodock reveal reductions in both stability and cofactor binding affinity of these two mutants. Comparative molecular dynamics (MD) simulations were performed to evaluate the changes in dynamic properties of P5CR upon mutations. The results reveal that the two mutations enhance the rigidity of P5CR structure, especially that of cofactor binding site, which could result in decreased kinetics of cofactor entrance and egress. Comparison between the structural properties of the WT and mutants during MD simulations shows that the enhanced rigidity of mutants results most likely from the increased number of inter-atomic interactions and the decreased number of dynamic hydrogen bonds. Our study provides novel insight into the deleterious effects of the R119G and G206W mutations on P5CR, and sheds light on the mechanisms by which these mutations mediate Cutis Laxa.
Collapse
Affiliation(s)
- Peng Sang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Wei Hu
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yu-Jia Ye
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Lin-Hua Li
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Chao Zhang
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| | - Yue-Hui Xie
- b Department of Computer Science, The Faculty of Basic Medicine , Kunming Medical University , Kunming , P.R China
| | - Zhao-Hui Meng
- a Laboratory of Molecular Cardiology, Department of Cardiology , The First Affiliated Hospital of Kunming Medical University , Kunming , P.R. China
| |
Collapse
|
32
|
Yan R, Vuong TV, Wang W, Master ER. Action of a GH115 α-glucuronidase from Amphibacillus xylanus at alkaline condition promotes release of 4-O-methylglucopyranosyluronic acid from glucuronoxylan and arabinoglucuronoxylan. Enzyme Microb Technol 2017. [PMID: 28648176 DOI: 10.1016/j.enzmictec.2017.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glucuronic acid and/or 4-O-methyl-glucuronic acid (GlcA/MeGlcA) are substituents of the main xylans present in hardwoods, conifers, and many cereal grains. α-Glucuronidases from glycoside hydrolase family GH115 can target GlcA/MeGlcA from both internally and terminally substituted regions of xylans. The current study describes the first GH115 α-glucuronidase, AxyAgu115A, from the alkaliphilic organism Amphilbacillus xylanus. AxyAgu115A was active in a wide pH range, and demonstrated better performance in alkaline condition compared to other characterized GH115 α-glucuronidases, which generally show optimal activity in acidic conditions. Specifically, its relative activity between pH 5.0 and pH 8.5 was above 80%, and was 35% of maximum at pH 10.5; although the enzyme lost 30% and 80% relative residual activity after 24-h pre-incubation at pH 9 and pH 10, respectively. AxyAgu115A was also similarly active towards glucuronoxylan as well as comparatively complex xylans such as spruce arabinoglucurunoxylan. Accommodation of complex xylans was supported by docking analyses that predicted accessibility of AxyAgu115A to branched xylo-oligosaccharides. MeGlcA release by AxyAgu115A from each xylan sample was increased by up to 30% by performing the reaction at pH 11.0 rather than pH 4.0, revealing applied benefits of AxyAgu115A for xylan recovery and processing.
Collapse
Affiliation(s)
- Ruoyu Yan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Weijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada.
| |
Collapse
|
33
|
|
34
|
Sang P, Du X, Yang LQ, Meng ZH, Liu SQ. Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms. RSC Adv 2017. [DOI: 10.1039/c6ra23230b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The physicochemical bases for enzyme cold-adaptation remain elusive.
Collapse
Affiliation(s)
- Peng Sang
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources
- Yunnan University
- Kunming
- P. R. China
- Department of Biochemistry and Molecular Biology
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Shu-Qun Liu
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| |
Collapse
|
35
|
Tu T, Li Y, Su X, Meng K, Ma R, Wang Y, Yao B, Lin Z, Luo H. Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases. Sci Rep 2016; 6:38413. [PMID: 27929074 PMCID: PMC5143973 DOI: 10.1038/srep38413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparent Tms increased by 0.6-3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
Collapse
Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yeqing Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhemin Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| |
Collapse
|
36
|
Facile modulation of enantioselectivity of thermophilic Geobacillus zalihae lipase by regulating hydrophobicity of its Q114 oxyanion. Enzyme Microb Technol 2016; 93-94:174-181. [DOI: 10.1016/j.enzmictec.2016.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/20/2016] [Accepted: 08/30/2016] [Indexed: 01/04/2023]
|
37
|
Ben Bdira F, Jiang J, Kallemeijn W, de Haan A, Florea BI, Bleijlevens B, Boot R, Overkleeft HS, Aerts JM, Ubbink M. Hydrophobic Interactions Contribute to Conformational Stabilization of Endoglycoceramidase II by Mechanism-Based Probes. Biochemistry 2016; 55:4823-35. [DOI: 10.1021/acs.biochem.6b00363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Jianbing Jiang
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Wouter Kallemeijn
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Annett de Haan
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Bogdan I. Florea
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Boris Bleijlevens
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Rolf Boot
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Herman S. Overkleeft
- Department
of Bio-organic Synthesis, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Johannes M. Aerts
- Department of Medical Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department
of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| |
Collapse
|
38
|
Goyal B, Srivastava KR, Patel K, Durani S. Modulation of β-Hairpin Peptide Self-Assembly: A Twenty-Residue Poly-lβ-Hairpin Modified Rationally as a Mixed-l,dHydrolase. ChemistrySelect 2016. [DOI: 10.1002/slct.201600078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib- 140406 Punjab India
| | - Kinshuk Raj Srivastava
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Physics and Astronomy; Michigan State University; East Lansing USA
| | - Kirti Patel
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
- Department of Chemistry; N. B. Mehta Science College, Bordi, Dahanu; Dist. Thane Maharashtra India
| | - Susheel Durani
- Department of Chemistry; Indian Institute of Technology Bombay; Powai Mumbai- 400076 India
| |
Collapse
|
39
|
Ruiz DM, Turowski VR, Murakami MT. Effects of the linker region on the structure and function of modular GH5 cellulases. Sci Rep 2016; 6:28504. [PMID: 27334041 PMCID: PMC4917841 DOI: 10.1038/srep28504] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
The association of glycosyl hydrolases with catalytically inactive modules is a successful evolutionary strategy that is commonly used by biomass-degrading microorganisms to digest plant cell walls. The presence of accessory domains in these enzymes is associated with properties such as higher catalytic efficiency, extension of the catalytic interface and targeting of the enzyme to the proper substrate. However, the importance of the linker region in the synergistic action of the catalytic and accessory domains remains poorly understood. Thus, this study examined how the inter-domain region affects the structure and function of modular GH5 endoglucanases, by using cellulase 5A from Bacillus subtilis (BsCel5A) as a model. BsCel5A variants featuring linkers with different stiffnesses or sizes were designed and extensively characterized, revealing that changes in flexibility or rigidity in this region differentially affect kinetic behavior. Regarding the linker length, we found that precise inter-domain spacing is required to enable efficient hydrolysis because excessively long or short linkers were equally detrimental to catalysis. Together, these findings identify molecular and structural features that may contribute to the rational design of chimeric and multimodular glycosyl hydrolases.
Collapse
Affiliation(s)
- Diego M. Ruiz
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970, Brazil
| | - Valeria R. Turowski
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970, Brazil
| | - Mario T. Murakami
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas/SP, 13083-970, Brazil
| |
Collapse
|
40
|
Taghizadeh M, Goliaei B, Madadkar-Sobhani A. Variability of the Cyclin-Dependent Kinase 2 Flexibility Without Significant Change in the Initial Conformation of the Protein or Its Environment; a Computational Study. IRANIAN JOURNAL OF BIOTECHNOLOGY 2016; 14:1-12. [PMID: 28959320 DOI: 10.15171/ijb.1419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 (hCDK2) protein flexibility without affecting a significant change in its initial environment or the protein per se. OBJECTIVES The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations. MATERIALS AND METHODS Using Gromacs package (version 4.5.4), three independent molecular dynamics (MD) simulations of the hCDK2 protein (PDB ID: 1HCL) was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations (RMSF) calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas. RESULTS More than 50% of the variation in the flexibility (the distance between the maximum and the minimum amount of the RMSF) was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves. CONCLUSIONS This work has introduced a new class of flexibility aspect of the proteins' residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins' flexibility.
Collapse
Affiliation(s)
- Mohammad Taghizadeh
- Laboratory of Biophysics and Molecular Biology, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Bahram Goliaei
- Laboratory of Biophysics and Molecular Biology, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | |
Collapse
|
41
|
Boulton S, Melacini G. Advances in NMR Methods To Map Allosteric Sites: From Models to Translation. Chem Rev 2016; 116:6267-304. [PMID: 27111288 DOI: 10.1021/acs.chemrev.5b00718] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The last five years have witnessed major developments in the understanding of the allosteric phenomenon, broadly defined as coupling between remote molecular sites. Such advances have been driven not only by new theoretical models and pharmacological applications of allostery, but also by progress in the experimental approaches designed to map allosteric sites and transitions. Among these techniques, NMR spectroscopy has played a major role given its unique near-atomic resolution and sensitivity to the dynamics that underlie allosteric couplings. Here, we highlight recent progress in the NMR methods tailored to investigate allostery with the goal of offering an overview of which NMR approaches are best suited for which allosterically relevant questions. The picture of the allosteric "NMR toolbox" is provided starting from one of the simplest models of allostery (i.e., the four-state thermodynamic cycle) and continuing to more complex multistate mechanisms. We also review how such an "NMR toolbox" has assisted the elucidation of the allosteric molecular basis for disease-related mutations and the discovery of novel leads for allosteric drugs. From this overview, it is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
Collapse
Affiliation(s)
- Stephen Boulton
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology Department of Biochemistry and Biomedical Sciences, McMaster University , 1280 Main St. W., Hamilton L8S 4M1, Canada
| |
Collapse
|
42
|
de Cassia Pereira J, Travaini R, Paganini Marques N, Bolado-Rodríguez S, Bocchini Martins DA. Saccharification of ozonated sugarcane bagasse using enzymes from Myceliophthora thermophila JCP 1-4 for sugars release and ethanol production. BIORESOURCE TECHNOLOGY 2016; 204:122-129. [PMID: 26773948 DOI: 10.1016/j.biortech.2015.12.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/16/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
The saccharification of ozonated sugarcane bagasse (SCB) by enzymes from Myceliophthora thermophila JCP 1-4 was studied. Fungal enzymes provided slightly higher sugar release than commercial enzymes, working at 50°C. Sugar release increased with temperature increase. Kinetic studies showed remarkable glucose release (4.99 g/L, 3%w/w dry matter) at 60°C, 8 h of hydrolysis, using an enzyme load of 10 FPU (filter paper unit). FPase and β-glucosidase activities increased during saccharification (284% and 270%, respectively). No further significant improvement on glucose release was observed increasing the enzyme load above 7.5 FPU per g of cellulose. Higher dry matter contents increased sugars release, but not yields. The fermentation of hydrolysates by Saccharomyces cerevisiae provided glucose-to-ethanol conversions around to 63%.
Collapse
Affiliation(s)
- Josiani de Cassia Pereira
- Department of Biology, IBILCE/UNESP - Univ Estadual Paulista, Rua Cristóvão Colombo, 2265, 15054-000 São José do Rio Preto, São Paulo State, Brazil.
| | - Rodolfo Travaini
- Department of Chemical Engineering and Environmental Technology, University of Valladolid - UVa, Calle Doctor Mergelina, s/n, 47005 Valladolid, Spain.
| | - Natalia Paganini Marques
- Department of Biochemistry and Chemical Technology, IQ/UNESP - Univ Estadual Paulista, Rua Prof. Francisco Degni, 55, 14800-060 Araraquara, São Paulo State, Brazil.
| | - Silvia Bolado-Rodríguez
- Department of Chemical Engineering and Environmental Technology, University of Valladolid - UVa, Calle Doctor Mergelina, s/n, 47005 Valladolid, Spain.
| | - Daniela Alonso Bocchini Martins
- Department of Biochemistry and Chemical Technology, IQ/UNESP - Univ Estadual Paulista, Rua Prof. Francisco Degni, 55, 14800-060 Araraquara, São Paulo State, Brazil.
| |
Collapse
|
43
|
Kovacic F, Mandrysch A, Poojari C, Strodel B, Jaeger KE. Structural features determining thermal adaptation of esterases. Protein Eng Des Sel 2016; 29:65-76. [PMID: 26647400 PMCID: PMC5943684 DOI: 10.1093/protein/gzv061] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 11/14/2022] Open
Abstract
The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function.
Collapse
Affiliation(s)
- Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Agathe Mandrysch
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany
| | - Chetan Poojari
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| | - Birgit Strodel
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany Institute of Theoretical and Computational Chemistry, Heinrich-Heine-University Duesseldorf, D-40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426 Juelich, Germany Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Juelich GmbH, D-52426 Juelich, Germany
| |
Collapse
|
44
|
Hospital A, Goñi JR, Orozco M, Gelpí JL. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem 2015; 8:37-47. [PMID: 26604800 PMCID: PMC4655909 DOI: 10.2147/aabc.s70333] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
Collapse
Affiliation(s)
- Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain
| | - Josep Ramon Goñi
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain ; Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Josep L Gelpí
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| |
Collapse
|
45
|
Baer B, Millar AH. Proteomics in evolutionary ecology. J Proteomics 2015; 135:4-11. [PMID: 26453985 DOI: 10.1016/j.jprot.2015.09.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/22/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023]
Abstract
Evolutionary ecologists are traditionally gene-focused, as genes propagate phenotypic traits across generations and mutations and recombination in the DNA generate genetic diversity required for evolutionary processes. As a consequence, the inheritance of changed DNA provides a molecular explanation for the functional changes associated with natural selection. A direct focus on proteins on the other hand, the actual molecular agents responsible for the expression of a phenotypic trait, receives far less interest from ecologists and evolutionary biologists. This is partially due to the central dogma of molecular biology that appears to define proteins as the 'dead-end of molecular information flow' as well as technical limitations in identifying and studying proteins and their diversity in the field and in many of the more exotic genera often favored in ecological studies. Here we provide an overview of a newly forming field of research that we refer to as 'Evolutionary Proteomics'. We point out that the origins of cellular function are related to the properties of polypeptide and RNA and their interactions with the environment, rather than DNA descent, and that the critical role of horizontal gene transfer in evolution is more about coopting new proteins to impact cellular processes than it is about modifying gene function. Furthermore, post-transcriptional and post-translational processes generate a remarkable diversity of mature proteins from a single gene, and the properties of these mature proteins can also influence inheritance through genetic and perhaps epigenetic mechanisms. The influence of post-transcriptional diversification on evolutionary processes could provide a novel mechanistic underpinning for elements of rapid, directed evolutionary changes and adaptations as observed for a variety of evolutionary processes. Modern state-of the art technologies based on mass spectrometry are now available to identify and quantify peptides, proteins, protein modifications and protein interactions of interest with high accuracy and assess protein diversity and function. Therefore, proteomic technologies can be viewed as providing evolutionary biologist with exciting novel opportunities to understand very early events in functional variation of cellular molecular machinery that are acting as part of evolutionary processes.
Collapse
Affiliation(s)
- B Baer
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia.
| | - A H Millar
- Centre for Integrative Bee Research (CIBER) and ARC Centre of Excellence in Plant Energy Biology, Bayliss Building, The University of Western Australia, 6009 Crawley, Australia
| |
Collapse
|
46
|
Katz FS, Pecic S, Tran TH, Trakht I, Schneider L, Zhu Z, Ton-That L, Luzac M, Zlatanic V, Damera S, Macdonald J, Landry DW, Tong L, Stojanovic MN. Discovery of New Classes of Compounds that Reactivate Acetylcholinesterase Inhibited by Organophosphates. Chembiochem 2015; 16:2205-2215. [PMID: 26350723 DOI: 10.1002/cbic.201500348] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 11/11/2022]
Abstract
Acetylcholinesterase (AChE) that has been covalently inhibited by organophosphate compounds (OPCs), such as nerve agents and pesticides, has traditionally been reactivated by using nucleophilic oximes. There is, however, a clearly recognized need for new classes of compounds with the ability to reactivate inhibited AChE with improved in vivo efficacy. Here we describe our discovery of new functional groups--Mannich phenols and general bases--that are capable of reactivating OPC--inhibited AChE more efficiently than standard oximes and we describe the cooperative mechanism by which these functionalities are delivered to the active site. These discoveries, supported by preliminary in vivo results and crystallographic data, significantly broaden the available approaches for reactivation of AChE.
Collapse
Affiliation(s)
- Francine S Katz
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Stevan Pecic
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Timothy H Tran
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027 (USA)
| | - Ilya Trakht
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Laura Schneider
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Zhengxiang Zhu
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Long Ton-That
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Michal Luzac
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Viktor Zlatanic
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Shivani Damera
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Joanne Macdonald
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA).,Genecology Research Centre, Inflammation and Healing Research Cluster, School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD 4556 (Australia)
| | - Donald W Landry
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA)
| | - Liang Tong
- Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027 (USA)
| | - Milan N Stojanovic
- Department of Medicine/Division of Experimental Therapeutics, Columbia University Medical Center, 630 W. 168th Street, New York, NY 10032 (USA).,Departments of Biomedical Engineering and Systems Biology, Columbia University, 630 W. 168th street, New York, NY 10032 (USA)
| |
Collapse
|
47
|
Conformational variation of an extreme drug resistant mutant of HIV protease. J Mol Graph Model 2015; 62:87-96. [PMID: 26397743 DOI: 10.1016/j.jmgm.2015.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 11/24/2022]
Abstract
Molecular mechanisms leading to high level drug resistance have been analyzed for the clinical variant of HIV-1 protease bearing 20 mutations (PR20); which has several orders of magnitude worse affinity for tested drugs. Two crystal structures of ligand-free PR20 with the D25N mutation of the catalytic aspartate (PR20D25N) revealed three dimers with different flap conformations. The diverse conformations of PR20D25N included a dimer with one flap in a unique "tucked" conformation; directed into the active site. Analysis of molecular dynamics (MD) simulations of the ligand-free PR20 and wild-type enzymes showed that the mutations in PR20 alter the correlated interactions between two monomers in the dimer. The two flaps tend to fluctuate more independently in PR20 than in the wild type enzyme. Combining the results of structural analysis by X-ray crystallography and MD simulations; unusual flap conformations and weakly correlated inter-subunit motions may contribute to the high level resistance of PR20.
Collapse
|
48
|
Giménez-Dejoz J, Kolář MH, Ruiz FX, Crespo I, Cousido-Siah A, Podjarny A, Barski OA, Fanfrlík J, Parés X, Farrés J, Porté S. Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase. PLoS One 2015; 10:e0134506. [PMID: 26222439 PMCID: PMC4519324 DOI: 10.1371/journal.pone.0134506] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/09/2015] [Indexed: 02/02/2023] Open
Abstract
Human aldo-keto reductase 1B15 (AKR1B15) is a newly discovered enzyme which shares 92% amino acid sequence identity with AKR1B10. While AKR1B10 is a well characterized enzyme with high retinaldehyde reductase activity, involved in the development of several cancer types, the enzymatic activity and physiological role of AKR1B15 are still poorly known. Here, the purified recombinant enzyme has been subjected to substrate specificity characterization, kinetic analysis and inhibitor screening, combined with structural modeling. AKR1B15 is active towards a variety of carbonyl substrates, including retinoids, with lower kcat and Km values than AKR1B10. In contrast to AKR1B10, which strongly prefers all-trans-retinaldehyde, AKR1B15 exhibits superior catalytic efficiency with 9-cis-retinaldehyde, the best substrate found for this enzyme. With ketone and dicarbonyl substrates, AKR1B15 also shows higher catalytic activity than AKR1B10. Several typical AKR inhibitors do not significantly affect AKR1B15 activity. Amino acid substitutions clustered in loops A and C result in a smaller, more hydrophobic and more rigid active site in AKR1B15 compared with the AKR1B10 pocket, consistent with distinct substrate specificity and narrower inhibitor selectivity for AKR1B15.
Collapse
Affiliation(s)
- Joan Giménez-Dejoz
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Michal H. Kolář
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Francesc X. Ruiz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Alexandra Cousido-Siah
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Alberto Podjarny
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire-Centre de Biologie Intégrative, CNRS, INSERM, UdS, Illkirch CEDEX, France
| | - Oleg A. Barski
- Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| |
Collapse
|
49
|
Zhang R, Zhou J, Gao Y, Guan Y, Li J, Tang X, Xu B, Ding J, Huang Z. Molecular and biochemical characterizations of a new low-temperature active mannanase. Folia Microbiol (Praha) 2015; 60:483-92. [DOI: 10.1007/s12223-015-0391-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 04/01/2015] [Indexed: 10/23/2022]
|
50
|
Homologous ligands accommodated by discrete conformations of a buried cavity. Proc Natl Acad Sci U S A 2015; 112:5039-44. [PMID: 25847998 DOI: 10.1073/pnas.1500806112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Conformational change in protein-ligand complexes is widely modeled, but the protein accommodation expected on binding a congeneric series of ligands has received less attention. Given their use in medicinal chemistry, there are surprisingly few substantial series of congeneric ligand complexes in the Protein Data Bank (PDB). Here we determine the structures of eight alkyl benzenes, in single-methylene increases from benzene to n-hexylbenzene, bound to an enclosed cavity in T4 lysozyme. The volume of the apo cavity suffices to accommodate benzene but, even with toluene, larger cavity conformations become observable in the electron density, and over the series two other major conformations are observed. These involve discrete changes in main-chain conformation, expanding the site; few continuous changes in the site are observed. In most structures, two discrete protein conformations are observed simultaneously, and energetic considerations suggest that these conformations are low in energy relative to the ground state. An analysis of 121 lysozyme cavity structures in the PDB finds that these three conformations dominate the previously determined structures, largely modeled in a single conformation. An investigation of the few congeneric series in the PDB suggests that discrete changes are common adaptations to a series of growing ligands. The discrete, but relatively few, conformational states observed here, and their energetic accessibility, may have implications for anticipating protein conformational change in ligand design.
Collapse
|