-
Je něco špatně v tomto záznamu ?
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering
J. Planas-Iglesias, F. Opaleny, P. Ulbrich, J. Stourac, Z. Sanusi, GP. Pinto, A. Schenkmayerova, J. Byska, J. Damborsky, B. Kozlikova, D. Bednar
Jazyk angličtina Země Anglie, Velká Británie
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
Directory of Open Access Journals
od 2005
Free Medical Journals
od 1996
PubMed Central
od 1974
Europe PubMed Central
od 1974
Open Access Digital Library
od 1996-01-01 do 2030-12-31
Open Access Digital Library
od 1974-01-01
Open Access Digital Library
od 1996-01-01
Open Access Digital Library
od 1996-01-01
Medline Complete (EBSCOhost)
od 1996-01-01
Oxford Journals Open Access Collection
od 1996-01-01
ROAD: Directory of Open Access Scholarly Resources
od 1974
PubMed
35438789
DOI
10.1093/nar/gkac249
Knihovny.cz E-zdroje
- MeSH
- internet MeSH
- molekulární modely MeSH
- proteinové inženýrství MeSH
- proteiny * genetika chemie MeSH
- software * MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
Citace poskytuje Crossref.org
- 000
- 00000naa a2200000 a 4500
- 001
- bmc23010771
- 003
- CZ-PrNML
- 005
- 20230801132623.0
- 007
- ta
- 008
- 230718s2022 enk f 000 0|eng||
- 009
- AR
- 024 7_
- $a 10.1093/nar/gkac249 $2 doi
- 035 __
- $a (PubMed)35438789
- 040 __
- $a ABA008 $b cze $d ABA008 $e AACR2
- 041 0_
- $a eng
- 044 __
- $a enk
- 100 1_
- $a Planas-Iglesias, Joan $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic $1 https://orcid.org/0000000262792483
- 245 10
- $a LoopGrafter: a web tool for transplanting dynamical loops for protein engineering / $c J. Planas-Iglesias, F. Opaleny, P. Ulbrich, J. Stourac, Z. Sanusi, GP. Pinto, A. Schenkmayerova, J. Byska, J. Damborsky, B. Kozlikova, D. Bednar
- 520 9_
- $a 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.
- 650 12
- $a software $7 D012984
- 650 _2
- $a molekulární modely $7 D008958
- 650 12
- $a proteiny $x genetika $x chemie $7 D011506
- 650 _2
- $a proteinové inženýrství $7 D015202
- 650 _2
- $a internet $7 D020407
- 655 _2
- $a časopisecké články $7 D016428
- 655 _2
- $a práce podpořená grantem $7 D013485
- 700 1_
- $a Opaleny, Filip $u Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
- 700 1_
- $a Ulbrich, Pavol $u Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
- 700 1_
- $a Stourac, Jan $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
- 700 1_
- $a Sanusi, Zainab $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
- 700 1_
- $a Pinto, Gaspar P $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
- 700 1_
- $a Schenkmayerova, Andrea $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic $1 https://orcid.org/0000000308839866
- 700 1_
- $a Byska, Jan $u Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
- 700 1_
- $a Damborsky, Jiri $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic $1 https://orcid.org/0000000278488216 $7 mzk2006348900
- 700 1_
- $a Kozlikova, Barbora $u Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
- 700 1_
- $a Bednar, David $u Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic $u International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic $1 https://orcid.org/0000000268030340 $7 mub2010571008
- 773 0_
- $w MED00003554 $t Nucleic acids research $x 1362-4962 $g Roč. 50, č. W1 (2022), s. W465-W473
- 856 41
- $u https://pubmed.ncbi.nlm.nih.gov/35438789 $y Pubmed
- 910 __
- $a ABA008 $b sig $c sign $y p $z 0
- 990 __
- $a 20230718 $b ABA008
- 991 __
- $a 20230801132619 $b ABA008
- 999 __
- $a ok $b bmc $g 1963292 $s 1197036
- BAS __
- $a 3
- BAS __
- $a PreBMC-MEDLINE
- BMC __
- $a 2022 $b 50 $c W1 $d W465-W473 $e 2022Jul05 $i 1362-4962 $m Nucleic acids research $n Nucleic Acids Res $x MED00003554
- LZP __
- $a Pubmed-20230718