Computational approaches to shed light on molecular mechanisms in biological processes

Giorgio Moro; Laura Bonati; Maurizio Bruschi; Ugo Cosentino; Luca De Gioia; Pier Carlo Fantucci; Alessandro Pandini; Elena Papaleo; Demetrio Pitea; Gloria A. A. Saracino; Giuseppe Zampella

doi:10.1007/s00214-006-0203-4

Computational approaches to shed light on molecular mechanisms in biological processes

Giorgio Moro^*, Laura Bonati, Maurizio Bruschi, Ugo Cosentino, Luca De Gioia, Pier Carlo Fantucci, Alessandro Pandini, Elena Papaleo, Demetrio Pitea, Gloria A. A. Saracino, Giuseppe Zampella

^*Corresponding author for this work

Randall Centre of Cell & Molecular Biophysics

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

9 Citations (Scopus)

Abstract

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

Original language	English
Article number	N/A
Pages (from-to)	723-741
Number of pages	19
Journal	THEORETICAL CHEMISTRY ACCOUNTS
Volume	117
Issue number	5-6
DOIs	https://doi.org/10.1007/s00214-006-0203-4
Publication status	Published - May 2007

Keywords

prion protein peptide
3D-QSAR
protein structure prediction
protein structural flexibility
DFT calculations
catalysis
DENSITY-FUNCTIONAL THEORY
PRION PROTEIN-FRAGMENT
CONTAINING ENZYME CHLOROPEROXIDASE
FUNGUS CURVULARIA-INAEQUALIS
FE-ONLY HYDROGENASES
ACTIVE-SITE MODELS
SCRAPIE PRION
DYNAMICS SIMULATIONS
SECONDARY STRUCTURE
AH RECEPTOR

Access to Document

10.1007/s00214-006-0203-4

Cite this

@article{d89702e2b0fb40829ff7c2e2b117c446,

title = "Computational approaches to shed light on molecular mechanisms in biological processes",

abstract = "Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.",

keywords = "prion protein peptide, 3D-QSAR, protein structure prediction, protein structural flexibility, DFT calculations, catalysis, DENSITY-FUNCTIONAL THEORY, PRION PROTEIN-FRAGMENT, CONTAINING ENZYME CHLOROPEROXIDASE, FUNGUS CURVULARIA-INAEQUALIS, FE-ONLY HYDROGENASES, ACTIVE-SITE MODELS, SCRAPIE PRION, DYNAMICS SIMULATIONS, SECONDARY STRUCTURE, AH RECEPTOR",

author = "Giorgio Moro and Laura Bonati and Maurizio Bruschi and Ugo Cosentino and {De Gioia}, Luca and Fantucci, {Pier Carlo} and Alessandro Pandini and Elena Papaleo and Demetrio Pitea and Saracino, {Gloria A. A.} and Giuseppe Zampella",

year = "2007",

month = may,

doi = "10.1007/s00214-006-0203-4",

language = "English",

volume = "117",

pages = "723--741",

journal = "THEORETICAL CHEMISTRY ACCOUNTS",

issn = "1432-881X",

publisher = "Springer New York",

number = "5-6",

}

TY - JOUR

T1 - Computational approaches to shed light on molecular mechanisms in biological processes

AU - Moro, Giorgio

AU - Bonati, Laura

AU - Bruschi, Maurizio

AU - Cosentino, Ugo

AU - De Gioia, Luca

AU - Fantucci, Pier Carlo

AU - Pandini, Alessandro

AU - Papaleo, Elena

AU - Pitea, Demetrio

AU - Saracino, Gloria A. A.

AU - Zampella, Giuseppe

PY - 2007/5

Y1 - 2007/5

N2 - Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

AB - Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

KW - prion protein peptide

KW - 3D-QSAR

KW - protein structure prediction

KW - protein structural flexibility

KW - DFT calculations

KW - catalysis

KW - DENSITY-FUNCTIONAL THEORY

KW - PRION PROTEIN-FRAGMENT

KW - CONTAINING ENZYME CHLOROPEROXIDASE

KW - FUNGUS CURVULARIA-INAEQUALIS

KW - FE-ONLY HYDROGENASES

KW - ACTIVE-SITE MODELS

KW - SCRAPIE PRION

KW - DYNAMICS SIMULATIONS

KW - SECONDARY STRUCTURE

KW - AH RECEPTOR

U2 - 10.1007/s00214-006-0203-4

DO - 10.1007/s00214-006-0203-4

M3 - Literature review

SN - 1432-881X

VL - 117

SP - 723

EP - 741

JO - THEORETICAL CHEMISTRY ACCOUNTS

JF - THEORETICAL CHEMISTRY ACCOUNTS

IS - 5-6

M1 - N/A

ER -

Computational approaches to shed light on molecular mechanisms in biological processes

Abstract

Keywords

Access to Document

Fingerprint

Cite this