List of works - Federico Fogolari

A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators

scientific article

A differential equation for the Generalized Born radii

scientific article published in June 2013

A new germline VHL gene mutation in three patients with apparently sporadic pheochromocytoma.

scientific article published in March 2013

A specific nanobody prevents amyloidogenesis of D76N β2-microglobulin in vitro and modifies its tissue distribution in vivo.

scientific article

Absolute quantification of choline-related biomarkers in breast cancer biopsies by liquid chromatography electrospray ionization mass spectrometry.

scientific article

Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes

scientific article published on 8 January 2015

Accurate Estimation of the Entropy of Rotation-Translation Probability Distributions

scientific article published on 24 November 2015

Agent-based protein structure prediction

Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

scientific article

Analysis of the conformation and stability of rat TTF-1 homeodomain by circular dichroism

scientific article published on 01 November 1994

Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics

scientific article

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.

scientific article published in April 2005

Automation of peak-tracking analysis of stepwise perturbed NMR spectra

scientific article published on 17 February 2017

Bluues server: electrostatic properties of wild-type and mutated protein structures.

scientific article

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

scientific article

CLP-based protein fragment assembly

Chelating effect in short polymers for the design of bidentate binders of increased affinity and selectivity

scientific article published on 26 October 2015

Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants

scientific article published on 01 March 2018

Citrate-stabilized gold nanoparticles hinder fibrillogenesis of a pathological variant of β2-microglobulin.

scientific article published on 7 March 2017

Collagen plays an active role in the aggregation of beta2-microglobulin under physiopathological conditions of dialysis-related amyloidosis

scientific article published in Journal of Biological Chemistry

Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: binding modes and drug resistance to a diketo acid inhibitor.

scientific article

Comparison of the structural and functional properties of RNase A and BS-RNase: a stepwise mutagenesis approach.

scientific article

Conformational stability of neuroglobin helix F--possible effects on the folding pathway within the globin family

scientific article

Conformational study of a short Pertussis toxin T cell epitope incorporated in a multiple antigen peptide template by CD and two-dimensional NMR. Analysis of the structural effects on the activity of synthetic immunogens

scientific article published on October 1993

Constraint Logic Programming approach to protein structure prediction

scientific article

Determining the energy landscape of proteins by a fast isotope exchange NMR approach.

scientific article published on 5 March 2012

Dimerization, stability and electrostatic properties of porcine beta-lactoglobulin.

scientific article

Dimers of mitochondrial ATP synthase form the permeability transition pore

scientific article

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

scientific article

Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations.

scientific article

EF loop conformational change triggers ligand binding in beta-lactoglobulins

scientific article

Effect of tetracyclines on the dynamics of formation and destructuration of beta2-microglobulin amyloid fibrils

scientific article

Electric dipole reorientation in the interaction of botulinum neurotoxins with neuronal membranes

scientific article published on 02 July 2009

Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA ⬇️

scientific article published on November 28, 1997

Electrostatic effects in homeodomain-DNA interactions

scientific article published in March 1997

Electrostatic properties of bovine beta-lactoglobulin

scientific article published on 01 June 2000

Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the <i>k</i>th Nearest Neighbor Method

scientific article published on 16 April 2021

Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange

scientific article

Estimation of $$^{3}J_{HN\hbox{-}H\alpha}$$ and $$^{3}J_{H\alpha\hbox{-}H\beta}$$ coupling constants from heteronuclear TOCSY spectra

scientific article published on 01 November 2007

Evaluation of J Coupling Constants from Peak Amplitudes of Total Correlation Spectra

Exploring exchange processes in proteins by paramagnetic perturbation of NMR spectra

scientific article published on 01 March 2020

Fast structure similarity searches among protein models: efficient clustering of protein fragments

scientific article published on 29 May 2012

Folding and fibrillogenesis: clues from beta2-microglobulin.

scientific article published on 15 June 2010

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

scientific article published on 8 February 2018

Free energies calculated according to Manning's polyelectrolyte model compared with Poisson Boltzmann predictions.

scientific article published in December 1993

From ATP to PTP and Back: A Dual Function for the Mitochondrial ATP Synthase

scientific article

Functional analysis of a novel RUNX2 missense mutation found in a family with cleidocranial dysplasia

scientific article published on 22 October 2005

Generalized Born forces: surface integral formulation

scientific article published in February 2013

Helix mobility and recognition function of the rat thyroid transcription factor 1 homeodomain - hints from 15N-NMR relaxation studies

article

Hydrogen-deuterium exchange studies of the rat thyroid transcription factor 1 homeodomain

scientific article published on June 1, 1997

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes

scientific article

Improved Processing of Selective NMR Spectra of Biopolymers by Separation of Noise and Signal Subspaces through Singular-Value Decomposition

scientific article published on 01 November 1996

Insights into a Protein-Nanoparticle System by Paramagnetic Perturbation NMR Spectroscopy

scientific article published on 07 November 2020

Interference of citrate-stabilized gold nanoparticles with β2-microglobulin oligomeric association

scientific article published on 01 May 2018

Investigations of Sso7d catalytic residues by NMR titration shifts and electrostatic calculations

scientific article

Limiting-laws of polyelectrolyte solutions. Ionic distribution in mixed-valency counterions systems. I: The model

scientific article published on 01 October 1991

MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: Free energy gradients in conformational transitions?

scientific article published on 01 April 2005

Mitochondrial F(0) F(1) -ATP synthase is a molecular target of 3-iodothyronamine, an endogenous metabolite of thyroid hormone

scientific article published on August 2012

Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.

scientific article published on March 1996

Molecular analysis of a human PAX6 homeobox mutant

scientific article published on June 2006

Molecular dynamics simulation of β2-microglobulin in denaturing and stabilizing conditions

scientific article published on 22 December 2010

Molecular dynamics simulation suggests possible interaction patterns at early steps of beta2-microglobulin aggregation.

scientific article published on 8 December 2006

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.

scientific article

Molecular mechanics and dynamics of biomolecules using a solvent continuum model

scientific article published in November 2001

Molecular models for intrastrand DNA G-quadruplexes

scientific article

Monitoring the interaction between β2-microglobulin and the molecular chaperone αB-crystallin by NMR and mass spectrometry: αB-crystallin dissociates β2-microglobulin oligomers.

scientific article published on 03 May 2013

NMR and circular dichroism studies of the lantibiotic nisin in non-aqueous environments.

scientific article published on March 1993

NMR dynamic studies suggest that allosteric activation regulates ligand binding in chicken liver bile acid-binding protein

scientific article

NMR solution structure of viscotoxin C1 from Viscum album species Coloratum ohwi: toward a structure-function analysis of viscotoxins

scientific article

NMR structural characterization of the reaction product between d(GpG) and the octahedral antitumor complex trans-RuCl2(DMSO)4

scientific article published on 01 August 1992

NMR structural determination of viscotoxin A3 from Viscum album L

scientific article

NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1

scientific article

Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein beta2-microglobulin revealed by real-time two-dimensional NMR.

scientific article published on 22 December 2009

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

article

OSCP subunit of mitochondrial ATP synthase: Role in regulation of enzyme function and of its transition to a pore

scholarly article by Valentina Giorgio et al published 6 October 2018 in British Journal of Pharmacology

On the variational approach to Poisson–Boltzmann free energies

PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles

scientific article published on 06 July 2018

Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands

scientific article

Polyelectrolytes in mixed salts: Scatchard plots obtained by means of Poisson-Boltzmann calculations

Presence of dityrosine bridges in thyroglobulin and their relationship with iodination.

scientific article published on July 1994

Probing the influence of citrate-capped gold nanoparticles on an amyloidogenic protein

scientific article published on 4 March 2015

Protein Aggregation Measurement through Electrical Impedance Spectroscopy

Protocol for MM/PBSA molecular dynamics simulations of proteins

scientific article published on July 2003

Proton Strong Coupling in Heteronuclear Systems. Theoretical and Experimental Evaluation in Quantitative Analysis of SQC NOESY Spectra of Biopolymers

Quantitative correlation of solvent polarity with the alpha-/3(10)-helix equilibrium: a heptapeptide behaves as a solvent-driven molecular spring

scientific article published in July 2003

Rapid oligomer formation of human muscle acylphosphatase induced by heparan sulfate.

scientific article published on 22 April 2012

Reduction of conformational mobility and aggregation in W60G β2-microglobulin: assessment by 15N NMR relaxation.

scientific article published on 18 October 2013

Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels

scientific article published on 4 May 2015

Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC)

scientific article

SIRT1 gene expression upon genotoxic damage is regulated by APE1 through nCaRE-promoter elements.

scientific article published on 19 December 2013

Scoring predictive models using a reduced representation of proteins: model and energy definition.

scientific article

Secondary structure effects on the interaction of different polynucleotides with Ca2+

scientific article published in 1990

Short-Chain Alkanethiol Coating for Small-Size Gold Nanoparticles Supporting Protein Stability

Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data.

scientific article

Simulation of electrostatic effects in Fab-antigen complex formation

scientific article published in August 2000

Single-shot NMR measurement of protein unfolding landscapes.

scientific article published on 13 April 2012

Solution structure of beta(2)-microglobulin and insights into fibrillogenesis.

scientific article

Structural and dynamics characteristics of acylphosphatase from Sulfolobus solfataricus in the monomeric state and in the initial native-like aggregates

scientific article published on 11 March 2010

Structural study of rat thyroid transcription factor 1 homeodomain (TTF-1 HD) by nuclear magnetic resonance

scientific article published on 01 December 1993

Structure, folding dynamics, and amyloidogenesis of D76N β2-microglobulin: roles of shear flow, hydrophobic surfaces, and α-crystallin.

scientific article published on 06 September 2013

Studying interactions by molecular dynamics simulations at high concentration

scientific article published on 22 February 2012

The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation

scientific article

The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology

scientific article

The Solution Structure of DNA-free Pax-8 Paired Box Domain Accounts for Redox Regulation of Transcriptional Activity in the Pax Protein Family

scientific article

The TTTT B lymphocyte stimulator promoter haplotype is associated with good response to rituximab therapy in seropositive rheumatoid arthritis resistant to tumor necrosis factor blockers.

scientific article published in January 2013

The catalytic site of glutathione peroxidases.

scientific article published in September 2008

The controlling roles of Trp60 and Trp95 in beta2-microglobulin function, folding and amyloid aggregation properties

scientific article

The interaction of β2-microglobulin with gold nanoparticles: impact of coating, charge and size

scientific article published on 06 September 2018

The oligomycin-sensitivity conferring protein of mitochondrial ATP synthase: emerging new roles in mitochondrial pathophysiology

scientific article published on 30 April 2014

The projection analysis of NMR chemical shifts reveals extended EPAC autoinhibition determinants.

scientific article published on 7 February 2012

The unique histidine in OSCP subunit of F-ATP synthase mediates inhibition of the permeability transition pore by acidic pH.

scientific article published on 7 December 2017

The α4β1/EMILIN1 interaction discloses a novel and unique integrin-ligand type of engagement

scientific article published on 13 October 2017

Transcriptomic analysis unveils correlations between regulative apoptotic caspases and genes of cholesterol homeostasis in human brain

scientific article

Unfolding and refolding of bovine beta-lactoglobulin monitored by hydrogen exchange measurements.

scientific article

Use of Autocorrelation-Like Function to Improve the Performance of Linear-Prediction Parameter Estimators

Using Secondary Structure Information for Protein Folding in CLP( FD )1 1The work is partially supported by MIUR project: Automatic Aggregate –and number– Reasoning for Computing

pKaShift Effects on Backbone Amide Base-Catalyzed Hydrogen Exchange Rates in Peptides

scientific article published in 1998

List of works by Federico Fogolari

A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators

A differential equation for the Generalized Born radii

A new germline VHL gene mutation in three patients with apparently sporadic pheochromocytoma.

A specific nanobody prevents amyloidogenesis of D76N β2-microglobulin in vitro and modifies its tissue distribution in vivo.

Absolute quantification of choline-related biomarkers in breast cancer biopsies by liquid chromatography electrospray ionization mass spectrometry.

Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes

Accurate Estimation of the Entropy of Rotation-Translation Probability Distributions

Agent-based protein structure prediction

Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

Analysis of the conformation and stability of rat TTF-1 homeodomain by circular dichroism

Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics

Application of MM/PBSA colony free energy to loop decoy discrimination: toward correlation between energy and root mean square deviation.

Automation of peak-tracking analysis of stepwise perturbed NMR spectra

Bluues server: electrostatic properties of wild-type and mutated protein structures.

Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii

CLP-based protein fragment assembly

Chelating effect in short polymers for the design of bidentate binders of increased affinity and selectivity

Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants

Citrate-stabilized gold nanoparticles hinder fibrillogenesis of a pathological variant of β2-microglobulin.

Collagen plays an active role in the aggregation of beta2-microglobulin under physiopathological conditions of dialysis-related amyloidosis

Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: binding modes and drug resistance to a diketo acid inhibitor.

Comparison of the structural and functional properties of RNase A and BS-RNase: a stepwise mutagenesis approach.

Conformational stability of neuroglobin helix F--possible effects on the folding pathway within the globin family

Conformational study of a short Pertussis toxin T cell epitope incorporated in a multiple antigen peptide template by CD and two-dimensional NMR. Analysis of the structural effects on the activity of synthetic immunogens

Constraint Logic Programming approach to protein structure prediction

Determining the energy landscape of proteins by a fast isotope exchange NMR approach.

Dimerization, stability and electrostatic properties of porcine beta-lactoglobulin.

Dimers of mitochondrial ATP synthase form the permeability transition pore

Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations

Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations.

EF loop conformational change triggers ligand binding in beta-lactoglobulins

Effect of tetracyclines on the dynamics of formation and destructuration of beta2-microglobulin amyloid fibrils

Electric dipole reorientation in the interaction of botulinum neurotoxins with neuronal membranes

Electrostatic and non-electrostatic contributions to the binding free energies of anthracycline antibiotics to DNA ⬇️

Electrostatic effects in homeodomain-DNA interactions

Electrostatic properties of bovine beta-lactoglobulin

Entropy of Two-Molecule Correlated Translational-Rotational Motions Using the <i>k</i>th Nearest Neighbor Method

Equilibrium unfolding thermodynamics of beta2-microglobulin analyzed through native-state H/D exchange

Estimation of $$^{3}J_{HN\hbox{-}H\alpha}$$ and $$^{3}J_{H\alpha\hbox{-}H\beta}$$ coupling constants from heteronuclear TOCSY spectra

Evaluation of J Coupling Constants from Peak Amplitudes of Total Correlation Spectra

Exploring exchange processes in proteins by paramagnetic perturbation of NMR spectra

Fast structure similarity searches among protein models: efficient clustering of protein fragments

Folding and fibrillogenesis: clues from beta2-microglobulin.

Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

Free energies calculated according to Manning's polyelectrolyte model compared with Poisson Boltzmann predictions.

From ATP to PTP and Back: A Dual Function for the Mitochondrial ATP Synthase

Functional analysis of a novel RUNX2 missense mutation found in a family with cleidocranial dysplasia

Generalized Born forces: surface integral formulation

Helix mobility and recognition function of the rat thyroid transcription factor 1 homeodomain - hints from 15N-NMR relaxation studies

Hydrogen-deuterium exchange studies of the rat thyroid transcription factor 1 homeodomain

Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes

Improved Processing of Selective NMR Spectra of Biopolymers by Separation of Noise and Signal Subspaces through Singular-Value Decomposition

Insights into a Protein-Nanoparticle System by Paramagnetic Perturbation NMR Spectroscopy

Interference of citrate-stabilized gold nanoparticles with β2-microglobulin oligomeric association

Investigations of Sso7d catalytic residues by NMR titration shifts and electrostatic calculations

Limiting-laws of polyelectrolyte solutions. Ionic distribution in mixed-valency counterions systems. I: The model

MM/PBSA analysis of molecular dynamics simulations of bovine β-lactoglobulin: Free energy gradients in conformational transitions?

Mitochondrial F(0) F(1) -ATP synthase is a molecular target of 3-iodothyronamine, an endogenous metabolite of thyroid hormone

Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.

Molecular analysis of a human PAX6 homeobox mutant

Molecular dynamics simulation of β2-microglobulin in denaturing and stabilizing conditions

Molecular dynamics simulation suggests possible interaction patterns at early steps of beta2-microglobulin aggregation.

Molecular dynamics simulations of β2-microglobulin interaction with hydrophobic surfaces.

Molecular mechanics and dynamics of biomolecules using a solvent continuum model

Molecular models for intrastrand DNA G-quadruplexes

Monitoring the interaction between β2-microglobulin and the molecular chaperone αB-crystallin by NMR and mass spectrometry: αB-crystallin dissociates β2-microglobulin oligomers.

NMR and circular dichroism studies of the lantibiotic nisin in non-aqueous environments.

NMR dynamic studies suggest that allosteric activation regulates ligand binding in chicken liver bile acid-binding protein

NMR solution structure of viscotoxin C1 from Viscum album species Coloratum ohwi: toward a structure-function analysis of viscotoxins

NMR structural characterization of the reaction product between d(GpG) and the octahedral antitumor complex trans-RuCl2(DMSO)4

NMR structural determination of viscotoxin A3 from Viscum album L

NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1

Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein beta2-microglobulin revealed by real-time two-dimensional NMR.

Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

OSCP subunit of mitochondrial ATP synthase: Role in regulation of enzyme function and of its transition to a pore

On the variational approach to Poisson–Boltzmann free energies

PDB2ENTROPY and PDB2TRENT: Conformational and Translational–Rotational Entropy from Molecular Ensembles

Peptide models of folding initiation sites of bovine beta-lactoglobulin: identification of nativelike hydrophobic interactions involving G and H strands

Polyelectrolytes in mixed salts: Scatchard plots obtained by means of Poisson-Boltzmann calculations