Protein engineering and design

Blundell, T.L.; Elliott, Graham S.; Gardner, Stephen P.; Hubbard, Tim; Islam, Suhail A.; Johnson, Mark S.; Mantafounis, Dimitris; Murray‐Rust, Peter; Overington, John P.; Pitts, John; Šali, Andrej; Sibanda, B. L.; Singh, Juswinder; Sternberg, Michael J.E.; Sutcliffe, Michael J.; Thornton, Janet; Travers, Paul

doi:10.1098/rstb.1989.0059

Cited by 12 publications

(9 citation statements)

References 34 publications

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“…Altering the structures and functions of proteins in a bid to design and create proteins with superior applications and better stability compared to their natives are made possible through the inauguration of protein engineering678. The rise of this multidisciplinary technology saw the development of tools proficient in modifying proteins to augment stability, selectivity and catalytic activity of enzymatic proteins and at the same time allow for better efficiency in the design of novel drug molecules with desirable activities678.…”

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confidence: 99%

“…The rise of this multidisciplinary technology saw the development of tools proficient in modifying proteins to augment stability, selectivity and catalytic activity of enzymatic proteins and at the same time allow for better efficiency in the design of novel drug molecules with desirable activities678. Mimicking nature, protein engineering utilizes mutagenesis and sequence variation to change the physical and chemical properties of proteins to achieve desired applications1678.…”

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confidence: 99%

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Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Zhang

Lazim

2017

Sci Rep

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In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.

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confidence: 99%

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confidence: 99%

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Zhang

Lazim

2017

Sci Rep

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“…Deviation from proper (cp, $ ) compliance, however, causes the vectors obtained from [ Eq. (8) ] to fulfill neither of these conditions in general. Since the C,-angle bending term will take care of the vector sizes (zero bending energy implies peptide vectors of unit length), a suitable form for the C,-torsional energy expression is where the circumflex sign indicates unit vectors.…”

Section: Ideal Peptide Geometry Restoring Termsmentioning

confidence: 95%

“…( 6 ) and ( 7 ) we may express the peptide vectors m2 and l2 in terms of m, and 1, and their vector product. We obtain where the coefficients are given by Equations ( 8 ) together with ( 9 ) provide the means to directly find the peptide vectors from the positions of the CY carbons and the backbone torsional angles. This is a central ingredient, because peptide vectors will occur in various energy terms.…”

Section: Ideal Trans Peptide Geometrymentioning

confidence: 99%

Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units

Gerber

1992

Biopolymers

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SYNOPSISThe central ingredient of any structure modeling tool is a molecular model or force field that accounts for proper geometry and energy calculation. For protein and peptide modeling based on entire amino acids as building blocks, we describe a peptide force field in which each amino acid is represented by a single point in space, taken at the position of the acarbon atom. Apart from the positional coordinates, these units carry the two torsional angles cp and I ) as additional degrees of freedom to account for the orientations of the peptide links. While some of the energy terms are analogous to expressions in atomic force fields, the presence of the angular variables leads to fundamental differences with new features and additional terms with no atomic counterparts.The force field reproduces secondary structure elements with very good accuracy. Globular parts of tertiary packing stay near the experimental structures with a rms deviation in Ca positions of 0.1-0.3 nm and about 25' in cp and $, depending on the size of the structure.A tendency for larger discrepancies is observed in exposed loops or terminal segments the conformations of which may be strongly influenced by neighboring domains.Finally, a scope of possible applications is presented. They range from modeling activities, such as model building by homology, to coarse scanning of conformation space in conformation analysis and structure determination. An extension to a dynamics model would offer the possibility to eliminate the less interesting high-frequency modes that in all-atom force-field dynamics absorb most of the computational effort.

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“…Rational protein engineering or directed evolution methods have shown that careful selection of sites for mutagenesis could result in an enhancement of thermostability among mesostable enzymes [3]. In case of larger proteins such as PGA, identification of potential sites by these methods remains a challenging problem due to wide range of possible substitutions.…”

Section: Site-specific Sequence-based Consensus Approach For Thermostmentioning

confidence: 99%

Sequence and structure-based comparative analysis to assess, identify and improve the thermostability of penicillin G acylases

Panigrahi

Chand

Mukherji

et al. 2015

Journal of Industrial Microbiology and Biotechnology

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Penicillin acylases are enzymes employed by the pharmaceutical industry for the manufacture of semi-synthetic penicillins. There is a continuous demand for thermostable and alkalophilic enzymes in such applications. We have carried out a computational analysis of known penicillin G acylases (PGAs) in terms of their thermostable nature using various protein-stabilizing factors. While the presence of disulfide bridges was considered initially to screen putative thermostable PGAs from the database, various other factors such as high arginine to lysine ratio, less content of thermolabile amino acids, presence of proline in β-turns, more number of ion-pair and other non-bonded interactions were also considered for comparison. A modified consensus approach designed could further identify stabilizing residue positions by site-specific comparison between mesostable and thermostable PGAs. A most likely thermostable enzyme identified from the analysis was PGA from Paracoccus denitrificans (PdPGA). This was cloned, expressed and tested for its thermostable nature using biochemical and biophysical experiments. The consensus site-specific sequence-based approach predicted PdPGA to be more thermostable than Escherichia coli PGA, but not as thermostable as the PGA from Achromobacter xylosoxidans. Experimental data showed that PdPGA was comparatively less thermostable than Achromobacter xylosoxidans PGA, although thermostability factors favored a much higher stability. Despite being mesostable, PdPGA being active and stable at alkaline pH is an advantage. Finally, several residue positions could be identified in PdPGA, which upon mutation selectively could improve the thermostability of the enzyme.

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Protein engineering and design

Cited by 12 publications

References 34 publications

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

Peptide mechanics: A force field for peptides and proteins working with entire residues as smallest units

Sequence and structure-based comparative analysis to assess, identify and improve the thermostability of penicillin G acylases

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