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1

The enzymatic mechanism of carboxypeptidase: A molecular dynamics study

Lucia Banci, Dr. Ivano Bertini, Giovanni La Penna

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1994

Language:

english

File:

PDF, 845 KB

english, 1994

2

Learning chemistry with multiple first-principles simulations

La Penna, Giovanni, Hureau, Christelle, Faller, Peter

Journal:

Molecular Simulation

Year:

2015

Language:

english

File:

PDF, 191 KB

english, 2015

3

Towards a high-throughput modelling of copper reactivity induced by structural disorder in amyloid peptides

La Penna, Giovanni, Mai Suan, Li

Journal:

Chemistry - A European Journal

Year:

2017

Language:

english

File:

PDF, 1.73 MB

english, 2017

4

Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: First-order mode-coupling approximation

Giovanni La Penna, Michele Mormino, Franco Pioli, Angelo Perico, Roberto Fioravanti, James M. Gruschus, James A. Ferretti

Journal:

Year:

1999

Language:

english

File:

PDF, 330 KB

english, 1999

5

Mode-coupling Smoluchowski dynamics of a double-stranded DNA oligomer

Simone Fausti, Giovanni La Penna, Carla Cuniberti, Angelo Perico

Journal:

Year:

1999

Language:

english

File:

PDF, 258 KB

english, 1999

6

Smoluchowski dynamics of the vnd/NK-2 homeodomain from Drosophila melanogaster: Second-order maximum correlation approximation

Giovanni La Penna, S. Fausti, Angelo Perico, J. A. Ferretti

Journal:

Year:

2000

Language:

english

File:

PDF, 195 KB

english, 2000

7

Electrostatic interactions with histone tails may bend linker DNA in chromatin

Angelo Perico, Giovanni La Penna, Luca Arcesi

Journal:

Year:

2006

Language:

english

File:

PDF, 212 KB

english, 2006

8

Modeling H3 histone N-terminal tail and linker DNA interactions

Giovanni La Penna, Sara Furlan, Angelo Perico

Journal:

Year:

2006

Language:

english

File:

PDF, 928 KB

english, 2006

9

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins

Luca Arcesi, Giovanni La Penna, Angelo Perico

Journal:

Year:

2007

Language:

english

File:

PDF, 241 KB

english, 2007

10

Erratum: “Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins”, Biopolymers 86, 127–135 (2007)

Luca Arcesi, Giovanni La Penna, Angelo Perico

Journal:

Year:

2008

Language:

english

File:

PDF, 36 KB

english, 2008

11

Hyaluronan chain conformation and dynamics

Sara Furlan, Giovanni La Penna, Angelo Perico, Attilio Cesàro

Journal:

Carbohydrate Research

Year:

2005

Language:

english

File:

PDF, 521 KB

english, 2005

12

Measuring electron sharing between atoms in first-principle simulations

Giovanni La Penna, Sara Furlan, Miquel Solà

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2011

Language:

english

File:

PDF, 311 KB

english, 2011

13

Ab initio simulations of Cu binding sites on the N-terminal region of prion protein

Sara Furlan, Giovanni La Penna, Francesco Guerrieri, Silvia Morante, Gian Carlo Rossi

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

2007

Language:

english

File:

PDF, 498 KB

english, 2007

14

Molecular statistics of cytochromec: structural plasticity and molecular environment

Giovanni La Penna, Sara Furlan, Lucia Banci

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

2007

Language:

english

File:

PDF, 495 KB

english, 2007

15

Modeling the interplay of glycine protonation and multiple histidine binding of copper in the prion protein octarepeat subdomains

Francesco Guerrieri, Velia Minicozzi, Silvia Morante, Giancarlo Rossi, Sara Furlan, Giovanni La Penna

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

2009

Language:

english

File:

PDF, 468 KB

english, 2009

16

The mechanism of hydrogen uptake in [NiFe] hydrogenase: first-principles molecular dynamics investigation of a model compound

Sara Furlan, Giovanni La Penna

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

2012

Language:

english

File:

PDF, 902 KB

english, 2012

17

Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory

Giovanni La Penna, Ayori Mitsutake, Masato Masuya, Yuko Okamoto

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 278 KB

english, 2003

18

The transition state in the isomerization of rhodopsin

Giovanni La Penna, Francesco Buda, Angelo Bifone, Huub J.M de Groot

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 162 KB

english, 1998

19

Modeling the dynamics of a mutated stem-loop in the SL1 domain of HIV-1Lai genomic RNA by 1H-NOESY spectra

Simone Fausti, Giovanni La Penna, Jacques Paoletti, Daniel Genest, Gérard Lancelot, Angelo Perico

Journal:

Journal of Biomolecular NMR

Year:

2001

Language:

english

File:

PDF, 219 KB

english, 2001

20

Wrapped-Around Models for the Lac Operon Complex

Giovanni La Penna, Angelo Perico

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 888 KB

english, 2010

21

Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements

Giannozzi, Paolo, Jansen, Karl, Penna, Giovanni La, Minicozzi, Velia, Morante, Silvia, Rossi, Giancarlo, Stellato, Francesco

Journal:

Year:

2012

Language:

english

File:

PDF, 2.38 MB

english, 2012

22

Metal ions and protons compete for ligand atoms in disordered peptides: Examples from computer simulations of copper binding to the prion tandem repeat

Sara Furlan, Giovanni La Penna

Journal:

Coordination Chemistry Reviews

Year:

2012

Language:

english

File:

PDF, 993 KB

english, 2012

23

Modeling of the Zn2+ binding in the 1–16 region of the amyloid β peptide involved in Alzheimer’s disease

Furlan, Sara, La Penna, Giovanni

Journal:

Physical Chemistry Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.95 MB

english, 2009

24

Modeling the Backbone Dynamics of Reduced and Oxidized Solvated Rat Microsomal Cytochrome b5

Giachetti, Andrea, Penna, Giovanni La, Perico, Angelo, Banci, Lucia

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 371 KB

english, 2004

25

Modeling Copper Binding to the Amyloid-β Peptide at Different pH: Toward a Molecular Mechanism for Cu Reduction

Furlan, Sara, Hureau, Christelle, Faller, Peter, La Penna, Giovanni

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 2.93 MB

english, 2012

26

Modeling the Cu + Binding in the 1−16 Region of the Amyloid-β Peptide Involved in Alzheimer’s Disease

Furlan, Sara, Hureau, Christelle, Faller, Peter, La Penna, Giovanni

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 2.37 MB

english, 2010

27

Metal Ions and Intrinsically Disordered Proteins and Peptides: From Cu/Zn Amyloid-β to General Principles

Faller, Peter, Hureau, Christelle, La Penna, Giovanni

Journal:

Accounts of Chemical Research

Year:

2014

Language:

english

File:

PDF, 2.14 MB

english, 2014

28

Modeling the Free Energy of Polypeptides in Different Environments

Furlan, Sara, La Penna, Giovanni, Perico, Angelo

Journal:

Year:

2008

Language:

english

File:

PDF, 362 KB

english, 2008

29

Anisotropic Internucleosome Interactions and Geometrical Constraints in the Organization of Chromatin

Cinacchi, Giorgio, La Penna, Giovanni, Perico, Angelo

Journal:

Year:

2007

Language:

english

File:

PDF, 776 KB

english, 2007

30

Conformational Dynamics of Hyaluronan Oligomers in Solution. 3. Molecular Dynamics from Monte Carlo Replica-Exchange Simulations and Mode-Coupling Diffusion Theory

Furlan, Sara, La Penna, Giovanni, Perico, Angelo, Cesàro, Attilio

Journal:

Year:

2004

Language:

english

File:

PDF, 276 KB

english, 2004

31

Ab Initio Molecular Dynamics of Heme in Cytochrome c

Furlan, Sara, La Penna, Giovanni, Banci, Lucia, Mealli, Carlo

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 365 KB

english, 2007

32

Dynamics of a Double Stranded DNA Oligomer: Mode-Coupling Diffusion Approach and Reduced Rigid Fragment Models

Penna, Giovanni La, Perico, Angelo, Genest, Daniel

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

2000

Language:

english

File:

PDF, 167 KB

english, 2000

33

Combined EPR and Molecular Modeling Study of PPI Dendrimers Interacting with Copper Ions: Effect of Generation and Maltose Decoration

Furlan, Sara, La Penna, Giovanni, Appelhans, Dietmar, Cangiotti, Michela, Ottaviani, Maria Francesca, Danani, Andrea

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 2.43 MB

english, 2014

34

Conformational Dynamics of Hyaluronan in Solution. 2. Mode-Coupling Diffusion Approach to Oligomers

Letardi, Sara, La Penna, Giovanni, Chiessi, Ester, Perico, Angelo, Cesàro, Attilio

Journal:

Year:

2002

Language:

english

File:

PDF, 404 KB

english, 2002

35

Identifying, By First-Principles Simulations, Cu[Amyloid-β] Species Making Fenton-Type Reactions in Alzheimer’s Disease

La Penna, Giovanni, Hureau, Christelle, Andreussi, Oliviero, Faller, Peter

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 3.51 MB

english, 2013

36

Molecular dynamics studies on superoxide dismutase and its mutants: the structural and functional role of Arg 143

Banci, Lucia, Carloni, Paolo, La Penna, Giovanni, Orioli, Pier Luigi

Journal:

Journal of the American Chemical Society

Year:

1992

Language:

english

File:

PDF, 1000 KB

english, 1992

37

Mode-Coupling Smoluchowski Dynamics of Polymers in the Limit of Rigid Structures

La Penna, Giovanni, Pratolongo, Roberto, Perico, Angelo

Journal:

Year:

1999

Language:

english

File:

PDF, 78 KB

english, 1999

38

A molecular dynamics study of carboxypeptidase A: effect of protonation of Glu 270

Banci, Lucia, Bertini, Ivano, La Penna, Giovanni

Journal:

Inorganic Chemistry

Year:

1993

Language:

english

File:

PDF, 439 KB

english, 1993

39

Exploring the Reactions of β-Amyloid (Aβ) Peptide 1–28 with Al III and Fe III Ions

Valensin, Daniela, Migliorini, Caterina, Valensin, Gianni, Gaggelli, Elena, La Penna, Giovanni, Kozlowski, Henryk, Gabbiani, Chiara, Messori, Luigi

Journal:

Inorganic Chemistry

Year:

2011

Language:

english

File:

PDF, 716 KB

english, 2011

40

Designing generalized statistical ensembles for numerical simulations of biopolymers

La Penna, Giovanni, Morante, Silvia, Perico, Angelo, Rossi, Gian Carlo

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 910 KB

english, 2004

41

A rigid core-flexible chain model for mesogenic molecules in molecular dynamics simulations of liquid crystals

La Penna, Giovanni, Catalano, Donata, Veracini, Carlo Alberto

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 542 KB

english, 1996

42

A constrained maximum entropy method in polymer statistics

La Penna, Giovanni

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 432 KB

english, 2003

43

Polyisoprene local dynamics in solution: Comparison between molecular dynamics simulations and high order diffusion theory

La Penna, Giovanni, Carbone, Paola, Carpentiero, Rita, Rapallo, Arnaldo, Perico, Angelo

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 365 KB

english, 2001

44

The shape dependence of the solute–solvent interactions in a liquid crystalline phase: A computer simulation study

La Penna, Giovanni, Foord, E. K., Emsley, J. W., Tildesley, D. J.

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 416 KB

english, 1996

45

AIP Conference Proceedings [AIP Publishing LLC INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2014 (ICCMSE 2014) - Athens, Greece (4–7 April 2014)] - A Cu-amyloid β complex activating Fenton chemistry in Alzheimer's disease: Learning with multiple first-principles simulations

La Penna, Giovanni, Hureau, Christelle, Faller, Peter

Year:

2014

Language:

english

File:

PDF, 195 KB

english, 2014

46

Dioxygen activation in Cu-amyloid β complex

Mirats, Andrea, Ali-Torres, Jorge, Rodríguez-Santiago, Luis, Sodupe, Mariona, La Penna, Giovanni

Journal:

Physical Chemistry Chemical Physics

Year:

2015

Language:

english

File:

PDF, 3.39 MB

english, 2015

47

Dynamics of macromolecules and nuclear magnetic relaxation: Application of mode-coupling diffusion theory to DNA, proteins and their complexes

Fausti, Simone, La Penna, Giovanni, Perico, Angelo, Pratolongo, Roberto

Journal:

Macromolecular Symposia

Year:

1999

Language:

english

File:

PDF, 199 KB

english, 1999

48

Diffusive Dynamics in a Detailed Potential: Application to Biological Macromolecules

Fausti, Simone, Penna, Giovanni La, Cuniberti, Carla, Perico, Angelo

Journal:

Molecular Simulation

Year:

2000

Language:

english

File:

PDF, 819 KB

english, 2000

49

Free Superoxide is an Intermediate in the Production of H 2 O 2 by Copper(I)-Aβ Peptide and O 2

Reybier, Karine, Ayala, Sara, Alies, Bruno, Rodrigues, João V., Bustos Rodriguez, Susana, La Penna, Giovanni, Collin, Fabrice, Gomes, Cláudio M., Hureau, Christelle, Faller, Peter

Journal:

Angewandte Chemie

Year:

2016

Language:

english

File:

PDF, 787 KB

english, 2016

50

Free Superoxide is an Intermediate in the Production of H 2 O 2 by Copper(I)-Aβ Peptide and O 2

Reybier, Karine, Ayala, Sara, Alies, Bruno, Rodrigues, João V., Bustos Rodriguez, Susana, La Penna, Giovanni, Collin, Fabrice, Gomes, Cláudio M., Hureau, Christelle, Faller, Peter

Journal:

Angewandte Chemie International Edition

Year:

2016

Language:

english

File:

PDF, 821 KB

english, 2016

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