De novo design of a non-local beta-sheet protein with high
stability and accuracy

J 2018

De novo design of a non-local beta-sheet protein with high stability and accuracy

MARCOS, E., T.M. CHIDYAUSIKU, A.C. MCSHAN, Thomas EVANGELIDIS, S. NERLI et. al.

Základní údaje

Originální název

De novo design of a non-local beta-sheet protein with high stability and accuracy

Autoři

MARCOS, E. (840 Spojené státy), T.M. CHIDYAUSIKU (840 Spojené státy), A.C. MCSHAN (840 Spojené státy), Thomas EVANGELIDIS (300 Řecko, domácí), S. NERLI (840 Spojené státy), L. CARTER (840 Spojené státy), L.G. NIVON (840 Spojené státy), A. DAVIS (840 Spojené státy), G. OBERDORFER (840 Spojené státy), Konstantinos TRIPSIANES (300 Řecko, garant, domácí), N.G. SGOURAKIS (840 Spojené státy) a D. BAKER (840 Spojené státy)

Vydání

NATURE STRUCTURAL & MOLECULAR BIOLOGY, NEW YORK, NATURE PUBLISHING GROUP, 2018, 1545-9993

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 12.109

Kód RIV

RIV/00216224:14740/18:00104596

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1038/s41594-018-0141-6

UT WoS

000449271800009

Klíčová slova anglicky

STRUCTURE PREDICTION; COMPUTATIONAL DESIGN; SECONDARY STRUCTURE; SOLENOID PROTEINS; SANDWICH PROTEIN; NEGATIVE DESIGN; CHEMICAL-SHIFTS; NMR; ROSETTA; VALIDATION

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 13. 3. 2019 13:12, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

beta-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-beta-sheet proteins from first principles lags far behind the design of all-alpha or mixed-alpha beta domains owing to their non-local nature and the tendency of exposed beta-strand edges to aggregate. Through study of loops connecting unpaired beta-strands (beta-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and beta-strand length that arise from hydrogen bonding and packing constraints on regular beta-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded beta-helices formed by eight antiparallel beta-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the beta-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local beta-sheet protein structures.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

MUNI/G/0739/2017, interní kód MU

Název: Pushing the limits in automated NMR structure determination using a single 4D NOESY spectrum and machine learning methods

Investor: Masarykova univerzita, Pushing the limits in automated NMR structure determination using a single 4D NOESY spectrum and machine learning methods, INTERDISCIPLINARY - Mezioborové výzkumné projekty

Citovat

MARCOS, E., T.M. CHIDYAUSIKU, A.C. MCSHAN, Thomas EVANGELIDIS, S. NERLI, L. CARTER, L.G. NIVON, A. DAVIS, G. OBERDORFER, Konstantinos TRIPSIANES, N.G. SGOURAKIS a D. BAKER. De novo design of a non-local beta-sheet protein with high stability and accuracy. NATURE STRUCTURAL & MOLECULAR BIOLOGY. NEW YORK: NATURE PUBLISHING GROUP, 2018, roč. 25, č. 11, s. 1028-1037. ISSN 1545-9993. Dostupné z: https://dx.doi.org/10.1038/s41594-018-0141-6.

@article{1471276,
   author = {Marcos, E. and Chidyausiku, T.M. and McShan, A.C. and Evangelidis, Thomas and Nerli, S. and Carter, L. and Nivon, L.G. and Davis, A. and Oberdorfer, G. and Tripsianes, Konstantinos and Sgourakis, N.G. and Baker, D.},
   article_location = {NEW YORK},
   article_number = {11},
   doi = {http://dx.doi.org/10.1038/s41594-018-0141-6},
   keywords = {STRUCTURE PREDICTION; COMPUTATIONAL DESIGN; SECONDARY STRUCTURE; SOLENOID PROTEINS; SANDWICH PROTEIN; NEGATIVE DESIGN; CHEMICAL-SHIFTS; NMR; ROSETTA; VALIDATION},
   language = {eng},
   issn = {1545-9993},
   journal = {NATURE STRUCTURAL & MOLECULAR BIOLOGY},
   title = {De novo design of a non-local beta-sheet protein with high stability and accuracy},
   volume = {25},
   year = {2018}
}

TY  - JOUR
ID  - 1471276
AU  - Marcos, E. - Chidyausiku, T.M. - McShan, A.C. - Evangelidis, Thomas - Nerli, S. - Carter, L. - Nivon, L.G. - Davis, A. - Oberdorfer, G. - Tripsianes, Konstantinos - Sgourakis, N.G. - Baker, D.
PY  - 2018
TI  - De novo design of a non-local beta-sheet protein with high stability and accuracy
JF  - NATURE STRUCTURAL & MOLECULAR BIOLOGY
VL  - 25
IS  - 11
SP  - 1028
EP  - 1028
PB  - NATURE PUBLISHING GROUP
SN  - 15459993
KW  - STRUCTURE PREDICTION
KW  - COMPUTATIONAL DESIGN
KW  - SECONDARY STRUCTURE
KW  - SOLENOID PROTEINS
KW  - SANDWICH PROTEIN
KW  - NEGATIVE DESIGN
KW  - CHEMICAL-SHIFTS
KW  - NMR
KW  - ROSETTA
KW  - VALIDATION
N2  - beta-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-beta-sheet proteins from first principles lags far behind the design of all-alpha or mixed-alpha beta domains owing to their non-local nature and the tendency of exposed beta-strand edges to aggregate. Through study of loops connecting unpaired beta-strands (beta-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and beta-strand length that arise from hydrogen bonding and packing constraints on regular beta-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded beta-helices formed by eight antiparallel beta-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the beta-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local beta-sheet protein structures.
ER  -

MARCOS, E., T.M. CHIDYAUSIKU, A.C. MCSHAN, Thomas EVANGELIDIS, S. NERLI, L. CARTER, L.G. NIVON, A. DAVIS, G. OBERDORFER, Konstantinos TRIPSIANES, N.G. SGOURAKIS a D. BAKER. De novo design of a non-local beta-sheet protein with high stability and accuracy. \textit{NATURE STRUCTURAL \&{}amp; MOLECULAR BIOLOGY}. NEW YORK: NATURE PUBLISHING GROUP, 2018, roč.~25, č.~11, s.~1028-1037. ISSN~1545-9993. Dostupné z: https://dx.doi.org/10.1038/s41594-018-0141-6.

Podrobný výpis o publikaci