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HotSpot Wizard: a web server for identification of hot spots in protein engineering

A. Pavelka, E. Chovancova, J. Damborsky
2009 Nucleic Acids Research  
HotSpot Wizard is a web server for automatic identification of 'hot spots' for engineering of substrate specificity, activity or enantioselectivity of enzymes and for annotation of protein structures.  ...  The HotSpot Wizard server should be useful for protein engineers interested in exploring the structure of their favourite protein and for the design of mutations in sitedirected mutagenesis and focused  ...  ACKNOWLEDGEMENTS We would like to express our thanks to the authors of the tools used by HotSpot Wizard and to Peter Lisak (Brno University of Technology) for the LLWS utility enabling a simple HTTP access  ... 
doi:10.1093/nar/gkp410 pmid:19465397 pmcid:PMC2703904 fatcat:lgix3nuohjg5hicsdnr33vj7aa

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
2018 Nucleic Acids Research  
HotSpot Wizard is a web server used for the automated identification of hotspots in semi-rational protein design to give improved protein stability, catalytic activity, substrate specificity and enantioselectivity  ...  HotSpot Wizard 3.0 now accepts the protein sequence as input data.  ...  FUNDING Ministry of Education, Youth and Sports of the Czech  ... 
doi:10.1093/nar/gky417 pmid:29796670 pmcid:PMC6030891 fatcat:qenwbseu3zg3hgkyabrd52rthq

Recent advances in user-friendly computational tools to engineer protein function

Carlos Eduardo Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovsky
2020 Briefings in Bioinformatics  
These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, proteinprotein and protein–nucleic acid interactions  ...  Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications.  ...  Likewise, the AlloSigMA web-server uses NMA aiming not only at the identification of hot-spots but also enabling evaluation of the effects of ligand binding or a mutation on allostery [49] (Figure 2C  ... 
doi:10.1093/bib/bbaa150 pmid:32743637 pmcid:PMC8138880 fatcat:4dmqbggn2nbsxcfzd4jg4rq6zy

ENGINEERING NON-HEME MONO- AND DIOXYGENASES FOR BIOCATALYSIS

Adi Dror, Ayelet Fishman
2012 Computational and Structural Biotechnology Journal  
This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities.  ...  It is concluded that knowledgebased protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic  ...  HotSpot Wizard is a web server designed for the identification of residues favorable for mutagenesis in the enzyme structure ("hot spots") [74] .  ... 
doi:10.5936/csbj.201209011 pmid:24688652 pmcid:PMC3962191 fatcat:74cyaiffczbi7d6iiq7gpqe44a

The Role of Surface Exposed Lysine in Conformational Stability and Functional Properties of Lipase from Staphylococcus Family

Nurul Nadirah Ahmad, Nor Hafizah Ahmad Kamarudin, Adam Thean Chor Leow, Raja Noor Zaliha Raja Abd. Rahman
2020 Molecules  
Surface charge residues have been recognized as one of the stability determinants in protein.  ...  Both mutants showed a 5 °C change in optimal temperature compared to their wild type.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/molecules25173858 pmid:32854267 fatcat:7tcjgtjapjeevdhe6gzoni75xm

Site-Directed Mutagenesis as Applied to Biocatalysts [chapter]

Juanita Yazmin, Gloria Saab-Rinco
2013 Genetic Manipulation of DNA and Protein - Examples from Current Research  
There is a server called HotSpot Wizard that combines information from extensive sequence and structure database searches with functional data to create a mutability map for a target protein.  ...  This approach was validated by comparing "hot spot" predictions with mutations extracted from the literature (Pavelka et al., 2009 ).  ... 
doi:10.5772/53330 fatcat:nw4f55xljndk7cf2tk25q2kzuy

Protein engineering of nirobenzene dioxygenase for enantioselective synthesis of chiral sulfoxides

J. Shainsky, K. Bernath-Levin, S. Isaschar-Ovdat, F. Glaser, A. Fishman
2013 Protein Engineering Design & Selection  
Mutagenesis at position 258 in the a-hydroxylase subunit of NBDO improved both activity and enantioselectivity.  ...  Cl-thioanisole vs. 5% for wild type).  ...  Acknowledgements We thank Dr Yuval Nov for assistance with the analysis and presentation of the screening results.  ... 
doi:10.1093/protein/gzt005 pmid:23442445 fatcat:kwogtg2zhzfgxa5oftianpwrom

Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology

Pavel Dvořák, Pablo I. Nikel, Jiří Damborský, Víctor de Lorenzo
2017 Biotechnology Advances  
We inspect a number of recent 24 strategies for catabolic pathway construction and optimization and we bring them together by 25 proposing an engineering workflow. 26 27  ...  In a twist of events, the last few years have 17 witnessed the emergence of new systemic fields (including systems and synthetic biology, and 18 metabolic engineering) that allow revisiting the same environmental  ...  HotSpot Wizard 2.0: automated design of site-specific mutations and smart 33 libraries in protein engineering. Nucleic Acids Res. 44, W479-487. Malcolm, L.T., Mann, G., Franks, A.E., 2015.  ... 
doi:10.1016/j.biotechadv.2017.08.001 pmid:28789939 fatcat:snmm6z3j4fajticae2sujhqxpe

ENVIRONMENTAL IMPACT ASSESSMENT OF ENERGY SAVING MEASURES IN BUILDINGS BY SIMAPRO8 SOFTWARE

L. D. Zahvoyska, M. I. Fedoruk
2017 Scientific Bulletin of UNFU  
The most important applications for an LCA are: • Identification of improvement opportunities through identifying environmental hot spots in the life cycle of a product. • Analysis of the contribution  ...  , and as a basis for environmental product declarations. • The basis for standardized metrics and the identification of Key Performance Indicators used in companies for life cycle management and decision  ...  Processes can have the following stages of development: • Blank: this is the default value when you create a new process or product stage • Temporary: this is meant for processes you put in as a quick  ... 
doi:10.15421/40270702 fatcat:mhtaimullbdwxalddoamnxic3u

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
Wigley for the contribution to this work with the x-ray structure of the protein ligand to the GR1222222.  ...  Dr Kontogiorgis Christos is thankful to the Foundation for Education and European Culture, established in Athens for the financial support of this postdoctoral research.  ...  In particular, we wanted to look at the "hot spot theory" (2) according to which only a few amino acids in a protein protein interface contribute strongly ("hot spots") while most of the interacting  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

1 Keynote address by Nobel Laureate Phillip A. Sharp the 21st century opened with a revolution in RNA biology

Phillip A. Sharp
2015 Journal of Biomolecular Structure and Dynamics  
The discoveries of RNA interference and the evolutionary conservation of microRNAs at the turn of the century heralded a revolution in RNA Biology and the development of important innovations.  ...  Excitingly, these insights and others are now being translated into new treatments for diseases and control of plant pathogens. 2 His Nobel Lecture and his speculative commentary on "What does the Future  ...  PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation. Molecular Carcinogenesis. (Epub ahead of print).  ... 
doi:10.1080/07391102.2015.1032624 fatcat:w7iil7k3ize77bjkthcyi52ohy

Science, society and biosafety of a field trial with transgenic biofuel poplars

Rebecca Van Acker, Véronique Storme, Geert Goeminne, Bart Ivens, René Custers, Dirk Aerts, Wim Soetaert, John Ralph, Nicholas Santoro, Jean-Charles Leplé, Gilles Pilate, Wout Boerjan
2011 BMC Proceedings  
A long history of quantitative genetic experimentation has established the genetic basis for many traits, which are likely adaptive since many of them are also correlated with environmental heterogeneity  ...  Recent applications of high-throughput sequencing and genotyping technologies to natural populations of forest Figure 1 (abstract I2) The distribution of Douglas-fir and loblolly pine in North America.  ...  The availability of the QMI to rapidly assess the potential risk generated by transgenic plants in characterized ecosystems, is a useful tool to assess the releasing or not of the permission of cultivation  ... 
doi:10.1186/1753-6561-5-s7-i23 fatcat:ulkxqgdupfdktkhsx2kba7pcn4

Protein-protein interactions: a structural bioinformatics approach

Sowmya Gopichandran
2022
PPIs are essential for catalysis, regulation, assembly, immunity and inhibition in a cell. However, it is unclear whether structural features can define protein functionality.  ...  The interface features were analysed for all non-redundant protein heterodimers (278) in the PDB.  ...  Michael Gromiha for valuable discussions. Acknowledgments G.S. is the recipient of an iMQRES PhD scholarship from Macquarie University. We are grateful to Dr.  ... 
doi:10.25949/19428407 fatcat:tiuh6dexzzehtifqiep4zgpqwu

A Generic Method for the Production of Recombinant Proteins in Escherichia coli Using a Dual Hexahistidine-Maltose-Binding Protein Affinity Tag [chapter]

Joseph E. Tropea, Scott Cherry, Sreedevi Nallamsetty, Christophe Bignon, David S. Waugh
2007 Msphere  
A generic protocol that utilizes a dual hexahistidine-maltose-binding protein (His 6 -MBP) affinity tag has been developed for the production of recombinant proteins in Escherichia coli.  ...  In the final step, the unwanted byproducts of the digest are absorbed by a second round of IMAC, leaving nothing but the pure passenger protein in the flow-through fraction.  ...  Istvan Botos for providing us with a photograph of Lon protease crystals (see Fig. 5 ).  ... 
doi:10.1007/978-1-59745-209-0_1 pmid:17272834 fatcat:3ytri6xm45fztgo5nz7i2o4ssy

Exporling the Evolvability of Old Yellow Enzymes for Organic Synthesis

Nathalie Nett, Hoebenreich, Sabrina (Dr.), Chemie
2019
Although systematic prediction of absolute enantioselectivity still remains for OYE variants, 'scaffold sampling' was confirmed as a fast engineering method for this family allow-ing access to new, potent  ...  Iden-tified hotspot positions of YqjM from Bacillus subtilis, i.e. C26D/I69T and C26G for improvement of activity and stereoselectivity, respectively, were transferred to seven OYE scaffolds.  ...  Identified hot spot residues of YqjM from Bacillus subtilis for the model compound 3-methylcyclohex-2-en-1-one, i.e.  ... 
doi:10.17192/z2017.0773 fatcat:2welf567g5fofjpiuclzmefapq
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