Comparison of ab Initio, DFT, and Semiempirical QM/MM
Approaches for Description of Catalytic Mechanism of Hairpin
Ribozyme

J 2014

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

MLÝNSKÝ, Vojtěch, Pavel BANÁŠ, Jiří ŠPONER, Marc W. VAN DER KAMP, Adrian J. MULHOLLAND et. al.

Basic information

Original name

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Authors

MLÝNSKÝ, Vojtěch (203 Czech Republic), Pavel BANÁŠ (203 Czech Republic), Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution), Marc W. VAN DER KAMP (826 United Kingdom of Great Britain and Northern Ireland), Adrian J. MULHOLLAND (826 United Kingdom of Great Britain and Northern Ireland) and Michal OTYEPKA (203 Czech Republic)

Edition

Journal of Chemical Theory and Computation, Washington DC, American Chemical Society, 2014, 1549-9618

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10403 Physical chemistry

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.498

RIV identification code

RIV/00216224:14740/14:00076678

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1021/ct401015e

UT WoS

000334571900024

Keywords in English

MOLECULAR-DYNAMICS SIMULATIONS; DELTA-VIRUS RIBOZYME; ACID-BASE CATALYSIS; TRANSITION-STATE STABILIZATION; DENSITY-FUNCTIONAL THEORY; ACTIVE-SITE ADENINE; ENZYME CATALYSIS; ALKALINE-PHOSPHATASE; SELF-CLEAVAGE; ELECTROSTATIC INTERACTIONS

Abstract

V originále

We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the g hairpin ribozyme by evaluating potential and free energy surfaces 4 of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid Which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Moller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.

Links

ED1.1.00/02.0068, research and development project

Name: CEITEC - central european institute of technology

Citovat

MLÝNSKÝ, Vojtěch, Pavel BANÁŠ, Jiří ŠPONER, Marc W. VAN DER KAMP, Adrian J. MULHOLLAND and Michal OTYEPKA. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. Journal of Chemical Theory and Computation. Washington DC: American Chemical Society, 2014, vol. 10, No 4, p. 1608-1622. ISSN 1549-9618. Available from: https://dx.doi.org/10.1021/ct401015e.

@article{1200031,
   author = {Mlýnský, Vojtěch and Banáš, Pavel and Šponer, Jiří and van der Kamp, Marc W. and Mulholland, Adrian J. and Otyepka, Michal},
   article_location = {Washington DC},
   article_number = {4},
   doi = {http://dx.doi.org/10.1021/ct401015e},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONS; DELTA-VIRUS RIBOZYME; ACID-BASE CATALYSIS; TRANSITION-STATE STABILIZATION; DENSITY-FUNCTIONAL THEORY; ACTIVE-SITE ADENINE; ENZYME CATALYSIS; ALKALINE-PHOSPHATASE; SELF-CLEAVAGE; ELECTROSTATIC INTERACTIONS},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme},
   url = {http://pubs.acs.org/doi/abs/10.1021/ct401015e},
   volume = {10},
   year = {2014}
}

TY  - JOUR
ID  - 1200031
AU  - Mlýnský, Vojtěch - Banáš, Pavel - Šponer, Jiří - van der Kamp, Marc W. - Mulholland, Adrian J. - Otyepka, Michal
PY  - 2014
TI  - Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme
JF  - Journal of Chemical Theory and Computation
VL  - 10
IS  - 4
SP  - 1608-1622
EP  - 1608-1622
PB  - American Chemical Society
SN  - 15499618
KW  - MOLECULAR-DYNAMICS SIMULATIONS
KW  - DELTA-VIRUS RIBOZYME
KW  - ACID-BASE CATALYSIS
KW  - TRANSITION-STATE STABILIZATION
KW  - DENSITY-FUNCTIONAL THEORY
KW  - ACTIVE-SITE ADENINE
KW  - ENZYME CATALYSIS
KW  - ALKALINE-PHOSPHATASE
KW  - SELF-CLEAVAGE
KW  - ELECTROSTATIC INTERACTIONS
UR  - http://pubs.acs.org/doi/abs/10.1021/ct401015e
L2  - http://pubs.acs.org/doi/abs/10.1021/ct401015e
N2  - We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the g hairpin ribozyme by evaluating potential and free energy surfaces 4 of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid Which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Moller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.
ER  -

MLÝNSKÝ, Vojtěch, Pavel BANÁŠ, Jiří ŠPONER, Marc W. VAN DER KAMP, Adrian J. MULHOLLAND and Michal OTYEPKA. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. \textit{Journal of Chemical Theory and Computation}. Washington DC: American Chemical Society, 2014, vol.~10, No~4, p.~1608-1622. ISSN~1549-9618. Available from: https://dx.doi.org/10.1021/ct401015e.

Detailed Information on Publication Record