List of works - Elena Papaleo

(Dis)similarity Index To Compare Correlated Motions in Molecular Simulations

scientific article published on 27 August 2015

A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast ⬇️

scientific article

A combined computational and structural model of the full-length human prolactin receptor

scientific article

A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks.

scientific article

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

scientific article

A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1).

scientific article published on 26 May 2017

A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation.

scientific article published on 31 October 2017

A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase

scientific article published on 22 July 2016

Absence of Neurofibromin Induces an Oncogenic Metabolic Switch via Mitochondrial ERK-Mediated Phosphorylation of the Chaperone TRAP1.

scientific article published in January 2017

Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level

scientific article published on 11 December 2019

An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations

scientific article published in August 2017

An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes

scientific article

An intrinsically disordered proteins community for ELIXIR

scientific article published on 15 October 2019

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

scientific article

Analyzing Biomolecular Ensembles

scientific article published on 01 January 2019

Atomistic Insights Into the Regulatory Mechanisms Mediated by Post- Translational Modifications: Molecular Dynamics Investigations

article published in 2012

C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes

scientific article published on 13 April 2012

C-type natriuretic peptide: Structural studies, fragment synthesis, and preliminary biological evaluation in human osteosarcoma cell lines.

scientific article published on January 2010

CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data

scientific article published on 16 March 2020

CECAM workshop on Intrinsically Disordered Proteins: Connecting Computation, Physics and Biology ETH Zürich September 2nd to 5th 2013.

scientific article published on 3 March 2014

CECAM workshop on intrinsically disordered proteins: Connecting computation, physics, and biology ETH Zürich September 2nd to 5th, 2013.

scientific article published on 12 December 2014

Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops

scientific article

Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain

scientific article published in May 2011

Comparing molecular dynamics force fields in the essential subspace.

scientific article

Computational Structural Biology of -nitrosylation of Cancer Targets

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

scientific article published on 07 November 2019

Computational approaches to shed light on molecular mechanisms in biological processes

scientific article

Conformational Changes and Free Energies in a Proline Isomerase

Conformational diseases: structural studies of aggregation of polyglutamine proteins

scientific article published on March 2011

Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: remodeling induced by mutation of calcium coordinating residues

scientific article published on 20 September 2010

Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase

scientific article published on 07 July 2012

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

scientific article

DisProt: intrinsic protein disorder annotation in 2020

scientific article published on 01 January 2020

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response

scientific article published on 20 August 2019

Dynamic Properties of a Psychrophilic α-Amylase in Comparison with a Mesophilic Homologue

scientific article published on 01 October 2009

Dynamic properties of extremophilic subtilisin-like serine-proteases

scientific article published on 27 January 2011

Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase

scientific article

E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft

scientific article

ENCORE: Software for Quantitative Ensemble Comparison.

scientific article published on 27 October 2015

ETHE1 mutations are specific to ethylmalonic encephalopathy

scientific article

Effects of Calcium Binding on Structure and Autolysis Regulation in Trypsins. A Molecular Dynamics Investigation.

scientific article

Evidence for the formation of a Mo-H intermediate in the catalytic cycle of formate dehydrogenase.

scientific article published on 16 July 2012

Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family

scientific article published on 01 July 2006

Flexibility of cold- and heat-adapted subtilisin-like serine proteinases evaluated with fluorescence quenching and molecular dynamics.

scientific article

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case

scientific article published on 6 February 2009

Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.

scientific article published in October 2012

Gaining insights into cancer biology through exploration of the cancer secretome using proteomic and bioinformatic tools.

scientific article

HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα

scientific article published in Nature Communications

High throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers

scientific article published on 11 November 2020

How well do force fields capture the strength of salt bridges in proteins?

scientific article published on 11 June 2018

Inhibitors of the Cdc34 acidic loop: A computational investigation integrating molecular dynamics, virtual screening and docking approaches.

scientific article published on 9 May 2014

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

scientific article

Interpreting pathways to discover cancer driver genes with Moonlight

scientific article published on 03 January 2020

Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

scientific article published on 22 November 2012

Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase

article

Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade

scientific article

MIR7-3HG, a MYC-dependent modulator of cell proliferation, inhibits autophagy by a regulatory loop involving AMBRA1.

scientific article published on 6 January 2017

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

scientific article published on 23 August 2016

Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation

scientific article

Molecular and structural insight into lysine selection on substrate and ubiquitin lysine 48 by the ubiquitin-conjugating enzyme Cdc34

scientific article published on 08 May 2013

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes

scientific article

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

scientific article published on 04 July 2018

Molecular dynamics investigation of cyclic natriuretic peptides: dynamic properties reflect peptide activity.

scientific article published on 7 March 2010

Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations

scientific article

Molecular dynamics simulation of chemokine receptors in lipid bilayer: a case study on C-C chemokine receptor type 2.

scientific article published on 10 August 2013

Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1

scientific article published on 14 March 2019

Moonlight: a tool for biological interpretation and driver genes discovery

article

Near Native-State Conformational Landscape of Psychrophilic and Mesophilic Enzymes: Probing the Folding Funnel Model

scientific article published on 01 June 2010

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

scientific article published on 05 March 2019

Optimization of electrostatics as a strategy for cold-adaptation: A case study of cold- and warm-active elastases

article

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

scientific article

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

scientific article

Protein aggregation: mechanisms and functional consequences.

scientific article published on 17 June 2012

Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.

scientific article

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins

scientific article published on 17 April 2014

Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila.

scientific article

Release of transcriptional repression via ErbB2-induced, SUMO-directed phosphorylation of myeloid zinc finger-1 serine 27 activates lysosome redistribution and invasion

scientific article published on 08 January 2019

Relevance of metal ions for lipase stability: structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion.

scientific article published on 25 July 2009

Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration

scientific article published on 30 June 2020

Selective autophagy maintains centrosome integrity and accurate mitosis by turnover of centriolar satellites

scientific article published on 13 September 2019

Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods.

scientific article

Structure-function investigation of 3-methylaspartate ammonia lyase reveals substrate molecular determinants for the deamination reaction

scientific article published on 21 May 2020

The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer.

scientific article

The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery

scientific article published on 18 February 2016

The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3.

scientific article published on 25 July 2013

The human Na(+)/H(+) exchanger 1 is a membrane scaffold protein for extracellular signal-regulated kinase 2

scientific article

The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase

scientific article published on 27 August 2014

The role of the central flexible region on the aggregation and conformational properties of human ataxin-3

scientific article

Three-dimensional structure of the catalytic domain of the yeast β-(1,3)-glucan transferase Gas1: a molecular modeling investigation

scientific article published on 21 October 2005

Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations

scientific article published on 25 January 2019

Use of Computational Biochemistry for Elucidating Molecular Mechanisms of Nitric Oxide Synthase

scientific article published on 23 March 2019

Validation of protein models by a neural network approach.

scientific article

Zinc induced folding is essential for TIM15 activity as an mtHsp70 chaperone

scientific article published on 11 October 2012

xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures

scientific article published on 05 July 2012

List of works by Elena Papaleo

(Dis)similarity Index To Compare Correlated Motions in Molecular Simulations

A Two-step Protein Quality Control Pathway for a Misfolded DJ-1 Variant in Fission Yeast ⬇️

A combined computational and structural model of the full-length human prolactin receptor

A comparative study of Whi5 and retinoblastoma proteins: from sequence and structure analysis to intracellular networks.

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1).

A single cysteine post-translational oxidation suffices to compromise globular proteins kinetic stability and promote amyloid formation.

A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase

Absence of Neurofibromin Induces an Oncogenic Metabolic Switch via Mitochondrial ERK-Mediated Phosphorylation of the Chaperone TRAP1.

Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level

An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations

An acidic loop and cognate phosphorylation sites define a molecular switch that modulates ubiquitin charging activity in Cdc34-like enzymes

An intrinsically disordered proteins community for ELIXIR

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

Analyzing Biomolecular Ensembles

Atomistic Insights Into the Regulatory Mechanisms Mediated by Post- Translational Modifications: Molecular Dynamics Investigations

Atomistic Insights Into the Regulatory Mechanisms Mediated by Post- Translational Modifications: Molecular Dynamics Investigations

C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes

C-type natriuretic peptide: Structural studies, fragment synthesis, and preliminary biological evaluation in human osteosarcoma cell lines.

CAncer bioMarker Prediction Pipeline (CAMPP)-A standardized framework for the analysis of quantitative biological data

CECAM workshop on Intrinsically Disordered Proteins: Connecting Computation, Physics and Biology ETH Zürich September 2nd to 5th 2013.

CECAM workshop on intrinsically disordered proteins: Connecting computation, physics, and biology ETH Zürich September 2nd to 5th, 2013.

Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops

Compaction properties of an intrinsically disordered protein: Sic1 and its kinase-inhibitor domain

Comparing molecular dynamics force fields in the essential subspace.

Computational Structural Biology of -nitrosylation of Cancer Targets

Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome

Computational approaches to shed light on molecular mechanisms in biological processes

Conformational Changes and Free Energies in a Proline Isomerase

Conformational diseases: structural studies of aggregation of polyglutamine proteins

Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: remodeling induced by mutation of calcium coordinating residues

Coupled motions during dynamics reveal a tunnel toward the active site regulated by the N-terminal α-helix in an acylaminoacyl peptidase

DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions

DisProt: intrinsic protein disorder annotation in 2020

Distinct signatures of lung cancer types: aberrant mucin O-glycosylation and compromised immune response

Dynamic Properties of a Psychrophilic α-Amylase in Comparison with a Mesophilic Homologue

Dynamic properties of extremophilic subtilisin-like serine-proteases

Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase

E2 superfamily of ubiquitin-conjugating enzymes: constitutively active or activated through phosphorylation in the catalytic cleft

ENCORE: Software for Quantitative Ensemble Comparison.

ETHE1 mutations are specific to ethylmalonic encephalopathy

Effects of Calcium Binding on Structure and Autolysis Regulation in Trypsins. A Molecular Dynamics Investigation.

Evidence for the formation of a Mo-H intermediate in the catalytic cycle of formate dehydrogenase.

Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family

Flexibility of cold- and heat-adapted subtilisin-like serine proteinases evaluated with fluorescence quenching and molecular dynamics.

Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case

Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics.

Gaining insights into cancer biology through exploration of the cancer secretome using proteomic and bioinformatic tools.

HUWE1 E3 ligase promotes PINK1/PARKIN-independent mitophagy by regulating AMBRA1 activation via IKKα

High throughput proteomics of breast cancer interstitial fluid: identification of tumor subtype-specific serologically relevant biomarkers

How well do force fields capture the strength of salt bridges in proteins?

Inhibitors of the Cdc34 acidic loop: A computational investigation integrating molecular dynamics, virtual screening and docking approaches.

Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.

Interpreting pathways to discover cancer driver genes with Moonlight

Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase

Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade

MIR7-3HG, a MYC-dependent modulator of cell proliferation, inhibits autophagy by a regulatory loop involving AMBRA1.

Mapping transiently formed and sparsely populated conformations on a complex energy landscape

Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation

Molecular and structural insight into lysine selection on substrate and ubiquitin lysine 48 by the ubiquitin-conjugating enzyme Cdc34

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes

Molecular dynamics ensemble refinement of the heterogeneous native state of NCBD using chemical shifts and NOEs

Molecular dynamics investigation of cyclic natriuretic peptides: dynamic properties reflect peptide activity.

Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations

Molecular dynamics simulation of chemokine receptors in lipid bilayer: a case study on C-C chemokine receptor type 2.

Molecular dynamics-guided discovery of an ago-allosteric modulator for GPR40/FFAR1

Moonlight: a tool for biological interpretation and driver genes discovery

Near Native-State Conformational Landscape of Psychrophilic and Mesophilic Enzymes: Probing the Folding Funnel Model

New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx

Optimization of electrostatics as a strategy for cold-adaptation: A case study of cold- and warm-active elastases

Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation

Predicting the impact of Lynch syndrome-causing missense mutations from structural calculations

Protein aggregation: mechanisms and functional consequences.

Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.

PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins

Reciprocal influence of protein domains in the cold-adapted acyl aminoacyl peptidase from Sporosarcina psychrophila.

Release of transcriptional repression via ErbB2-induced, SUMO-directed phosphorylation of myeloid zinc finger-1 serine 27 activates lysosome redistribution and invasion

Relevance of metal ions for lipase stability: structural rearrangements induced in the Burkholderia glumae lipase by calcium depletion.