Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies

Saravanan, P.; Dubey, Vikash Kumar; Patra, Sanjukta

doi:10.1007/s00894-014-2501-4

Cited by 3 publications

(2 citation statements)

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“…Site‐directed mutagenesis is a standard experimental technique used to generate site‐specific mutations in known protein‐coding genes . By deleting or substituting particular residues, the role of individual amino acids in the reaction mechanisms of enzymes or in the structural configuration of proteins can be studied .…”

Section: Introductionmentioning

confidence: 99%

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

et al. 2017

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(2017) 'Mutantelec : AnIn Silicomutation simulation platform for comparative electrostatic potential proling of proteins.', Journal of computational chemistry., 38 (7). pp. 467-474. Further information on publisher's website:https://doi.org/10.1002/jcc.24712 Publisher's copyright statement: This is the accepted version of the following article: Valdebenito-Maturana, Braulio, Reyes-Suarez, Jose Antonio, Henriquez, Jaime, Holmes, David S., Quatrini, Raquel, Pohl, Ehmke Arenas-Salinas, Mauricio (2017). Mutantelec: AnIn Silicomutation simulation platform for comparative electrostatic potential proling of proteins. Journal of Computational Chemistry 38(7): 467-474, which has been published in nal form at https://doi.org/10.1002/jcc.24712. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving. Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Journal of Computational Chemistry 30The electrostatic potential plays a key role in many biological processes like determining the affinity of a 31 ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. 32Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will

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Section: Introductionmentioning

confidence: 99%

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

et al. 2017

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“…[25][26][27] The effect of mutations on the biological activity of a protein can be better studied at the atomic level when explored theoretically; moreover, Molecular Dynamics (MD) simulations facilitate extensive analysis. [28][29][30][31] In this study, the molecular dynamics simulation of trimeric ORF1p was performed to gain insight into its structural dynamics. The important interactions responsible for mediating the 'lifted', 'twisted' and 'resting' positions of CTD were analyzed and reported in this study.…”

Section: Introductionmentioning

confidence: 99%

Conformational analysis on the wild type and mutated forms of human ORF1p: a molecular dynamics study

2015

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The protein ORF1p, encoded by the LINE-1 retrotransposon, is responsible for the packaging and transposition of its RNA transcript and is reported to be involved in various genetic disorders. The three domains of ORF1p co-ordinate together to facilitate the transposition, and the mechanism of nucleic acid binding is not yet clear. The C-terminal domain of ORF1p adopts a lifted, twisted or rested state, which is regulated by several inter- and intra-domain interactions that are explored in this study. The residues, Glu147, Asp151, Lys154, Arg261 and Tyr282, are majorly involved in mediating the functional dynamics of ORF1p by forming H-bonds and π-interactions. The importance of these residues was elucidated by performing molecular dynamics simulations on both native as well as mutated ORF1p. The Q147A-D151A-K154A mutant expressed unique dynamics featuring the lifting motion of the CTD core alone, while the R261A mutant resulted in the oscillatory motion of CTD. In both cases, the CTDs were held in place by Tyr282 and in its absence, the structural stability of CTDs in the trimeric unit was significantly affected. Additional interactions responsible for stabilizing the trimeric ORF1p to express its native dynamics were extracted in this study. The central role of Tyr282 in maintaining the functional state of ORF1p to facilitate nucleic acid binding and formation of ribonucleoprotein complex is well highlighted. The knowledge gained from this study forms the basis for understanding the nucleic acid binding mechanism of ORF1p, which could further provide additional support in exploring various genetic disorders.

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Thermostable lipases and their dynamics of improved enzymatic properties

Hamdan

Maiangwa

Ali

et al. 2021

Appl Microbiol Biotechnol

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Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed.

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Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies

Cited by 3 publications

References 40 publications

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins

Conformational analysis on the wild type and mutated forms of human ORF1p: a molecular dynamics study

Thermostable lipases and their dynamics of improved enzymatic properties

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