A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

Cristina Trujillo; Goar Sánchez-Sanz; Ibon Alkorta; José Elguero

doi:10.1007/s11224-012-0134-8

A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

Cristina Trujillo
, Goar Sánchez-Sanz
, Ibon Alkorta^*
, José Elguero

^*Corresponding author for this work

CSIC - Instituto de Química Médica

Research output: Contribution to journal › Article › peer-review

Abstract

Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4-5 kJ mol^-1.

Original language	English
Pages (from-to)	1145-1151
Number of pages	7
Journal	Structural Chemistry
Volume	24
Issue number	4
DOIs	https://doi.org/10.1007/s11224-012-0134-8
Publication status	Published - Aug 2013

Keywords

Cyclol
DFT calculations
GFP
Green fluorescent protein
Solvent effects
Water molecules

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10.1007/s11224-012-0134-8

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title = "A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model",

abstract = "Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4-5 kJ mol-1.",

keywords = "Cyclol, DFT calculations, GFP, Green fluorescent protein, Solvent effects, Water molecules",

author = "Cristina Trujillo and Goar S{\'a}nchez-Sanz and Ibon Alkorta and Jos{\'e} Elguero",

note = "Funding Information: Acknowledgments This work was supported by the Ministerio de Ciencia e Innovaci{\'o}n (Project No. CTQ2009-13129-C02-02) and Comunidad Aut{\'o}noma de Madrid (Project MADRISOLAR, ref. S-0505/PPQ/0225). The authors thank the CTI (CSIC) and the {\textquoteleft}{\textquoteleft}Centro de Computaci{\'o}n Cient{\'i}fica{\textquoteright}{\textquoteright} de la Universidad Aut{\'o}noma de Madrid for allocation of computer time.",

year = "2013",

month = aug,

doi = "10.1007/s11224-012-0134-8",

language = "English",

volume = "24",

pages = "1145--1151",

journal = "Structural Chemistry",

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T1 - A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

AU - Trujillo, Cristina

AU - Sánchez-Sanz, Goar

AU - Alkorta, Ibon

AU - Elguero, José

N1 - Funding Information: Acknowledgments This work was supported by the Ministerio de Ciencia e Innovación (Project No. CTQ2009-13129-C02-02) and Comunidad Autónoma de Madrid (Project MADRISOLAR, ref. S-0505/PPQ/0225). The authors thank the CTI (CSIC) and the ‘‘Centro de Computación Científica’’ de la Universidad Autónoma de Madrid for allocation of computer time.

PY - 2013/8

Y1 - 2013/8

N2 - Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4-5 kJ mol-1.

AB - Theoretical calculations at the B3LYP/6-311++G(d,p) level have been carried out on the reaction path connecting a dipeptide to an imidazolinone as a model for the formation of GFP. In addition, we have studied the hydration effects on the processes, adding a water molecule to assist the cyclization. The solvent effects have been taken into account by introducing the monohydrated molecules into a solvent cavity with a polarized continuum model. Significant reductions of the energy barriers for the reaction path can be observed within the water-assisted processes. The solvent effects account for a barrier lowering of 4-5 kJ mol-1.

KW - Cyclol

KW - DFT calculations

KW - GFP

KW - Green fluorescent protein

KW - Solvent effects

KW - Water molecules

UR - https://www.scopus.com/pages/publications/84880747274

U2 - 10.1007/s11224-012-0134-8

DO - 10.1007/s11224-012-0134-8

M3 - Article

AN - SCOPUS:84880747274

SN - 1040-0400

VL - 24

SP - 1145

EP - 1151

JO - Structural Chemistry

JF - Structural Chemistry

IS - 4

ER -

A theoretical investigation of the mechanism of formation of a simplified analog of the green fluorescent protein (GFP) from a peptide model

Abstract

Keywords

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