LoopGrafter: a web tool for transplanting dynamical loops for protein engineering

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00159816%3A_____%2F22%3A00077609" target="_blank" >RIV/00159816:_____/22:00077609 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14310/22:00126367

Result on the web

<a href="https://academic.oup.com/nar/article/50/W1/W465/6570728?login=true" target="_blank" >https://academic.oup.com/nar/article/50/W1/W465/6570728?login=true</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkac249" target="_blank" >10.1093/nar/gkac249</a>

Result language

angličtina

Original language name

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering

Original language description

The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses. [GRAPHICS] .

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Nucleic Acids Research

ISSN

0305-1048

e-ISSN

1362-4962

Volume of the periodical

50

Issue of the periodical within the volume

W1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

9

Pages from-to

"W465"-"W473"

UT code for WoS article

000785624300001

EID of the result in the Scopus database

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