PUBLICATIONS - ProteinPhysiologyLab

We like open science. We believe that exposure of the research process is likely to accelerate the overall progress of science.

You can find below links to our work in the form of papers, posters, research talks, lectures and grant applications. Peer reviews and the corresponding earlier versions of the work are included whenever available.

If some of it is useful to you, please cite us.

2018

PAPER "Frustration, function and folding" Current opinion in structural biology
PAPER "Localization of Energetic Frustration in Proteins" Methods in Molecular Biology (in press)
GRANT "ENIGMA: Evolution of Nanomachines In Geospheres and Microbial Ancestors" NAI (pending)

2017

POSTER "Revisiting the functional classification of class A beta-lactamases" data
PAPER "Inferring repeat-protein energetics from evolutionary information" PLoS computational biology
PAPER "The design of repeat proteins: Stability conflicts with functionality" Biochemistry & Molecular Biology Journal
PAPER "Degenerate cysteine patterns mediate two redox sensing mechanisms in the papillomavirus E7 oncoprotein" Redox Biology

PAPER "Hidden Structural Codes in Protein Intrinsic Disorder" Biochemistry

TALK "Do genome and proteome dynamics pose universal constraints to gene circuit design?" CMO-BIRS
TALK "Nothing in Biology makes sense except in the light of BS" CMO-BIRS
TALK "Structure, function and frustration in proteins: a conflicting origami" Biociencias Buenos Aires
TALKS "Frustration in proteins" IntInstPhysics, Natal, Brazil
TALK "Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics" ISMB
TALK "Structures, Symmetries and Energy Landscapes in the Ankyrin Repeat Protein Family" Protein Biophysics at the end of the world
GRANT "Termodinámica y evolución de proteínas repetitivas" ANPCyT (awarded)

GRANT "Folding made to measure: reprogramming the folding of repeat-proteins" Royal Society (awarded)
THESIS PhD "Desarrollo de métodos estadísticos para el análisis de patrones biológicos en proteínas: aplicaciones a familias de proteínas repetitivas" Rocío Espada - UBA

2016

PAPER "PEST Control of Molecular Stripping of NFκB from DNA Transcription Sites." J Phys Chem B
PAPER "Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics." Nucleic Acid Res
PAPER "Detailing protein landscapes under pressure" Biophysical Journal
PAPER "Protein Repeats from First Principles" Scientific Reports
PAPER "Optimal threshold estimation for binary classifiers using game theory" F1000Research
PAPER "Highlights from the 11th ISCB Student Council Symposium 2015" BMC-Bioinformatics
PAPER "Highlights of the 1st Argentine Symposium of Young Bioinformatics Researchers organized by the ISCB RSG-Argentina" PeerJ
POSTER "Disentangle structural information from sequence of repeat proteins"

ISCB Latam

POSTER "Disentangling structural information in amino acid sequences from repeat proteins"

qBio Conference

POSTER "Revisiting the functional classification of the serine beta lactamases A structural and energetic characterization" Latin American Protein Society Meeting - Rio de Janeiro, Brasil
POSTER "Análisis de la frustación energética local en sitios catalíticos de enzimas" 2E2B2C - BsAs
POSTER "Redesubriendo los patrones de secuencia y estructura en la familia de proteínas WD40" 2E2B2C - BsAs
POSTER "Evolution of protein motifs in the Early Region 1A protein of adenovirus" ISCB-LATAM meeting
POSTER "Conservation of sequence, structure and linear motifs within the intrinsically disordered and globular domains of the adenovirus E1A oncoprotein" ISCB-LATAM meeting
POSTER "Linear motif combination and a conserved flexible linker determine displacement ability of an intrinsically disordered viral oncoprotein" Gordon Research Conference Disordered proteins: From mechanisms to therapeutic opportunities
POSTER "INTRINSIC DISORDER AND BINDING PROPERTIES WITHIN LINEAR MOTIF-MEDIATED VIRAL AND CELLULAR RETINOBLASTOMA-TARGET PROTEIN INTERACTIONS" Gordon Research Conference Disordered proteins: From mechanisms to therapeutic opportunities

TALK "Frustration and the energy landscape of repeat proteins" GRC - protein folding dynamics
TALK "Inferring folding energy landscapes from repeat-protein sequences" NGP-NET, Belgrade
TALK "Frustración local y el paisaje energético de proteínas repetitivas" Protein Biophysics at the end of the world-Chile
THESIS PhD "Estructuras, Simetrías y Paisajes Energéticos en la Familia de Proteínas con Repeticiones

de Ankyrina

" R. Gonzalo Parra - UBA

2015

PAPER "Conformational heterogeneity determined by folding and oligomer assembly routes of the interferon response inhibitor NS1 protein" Biochemistry
PAPER "NGOME prediction of non-enzymatic protein deamidation from sequence-derived secondary structure and intrinsic disorder" PLoS ONE

PAPER "Capturing coevolutionary signals in repeat proteins" BMC Bioinformatics
PAPER "Repeat Proteins challenge the concept of structural domains" Biochem Soc Transact
PAPER "Structural and Energetic Characterization of the Ankyrin Repeat Protein Family" PLoS Comp Biol
PAPER "Synthetic Crossfeeding Cocultures in Yeast: Computational Model of Autoregulation and Design of a Tryptophan Export Device". Journal of Synthetic Biology.
PAPER "Convergent evolution and mimicry of protein linear motifs in host–pathogen interactions" Current Opinion in Structural Biology
POSTER "Estudio de la Frustración Local en β-lactamasas de clase A" SAB-SgoEstero
POSTER "NGOME prediction of non-enzymatic protein deamidation from sequence-derived secondary structure and intrinsic disorder" 10th Bioinformatics Benelux Conference
POSTER "Coevolución en proteínas repetitivas"

Workshop CELFI “La matemática como herramienta para entender la biología / La biología como fuente de problemas matemáticos”

POSTER "Local frustration and the energy landscapes of ankyrin repeat proteins"

ISMB

POSTER "PATENA an algorithm for the design of protein linker sequences"
POSTER "UN LINKER FLEXIBLE Y CONSERVADO POTENCIA LA AFINIDAD DEL DOMINIO VIRAL INTRINSECAMENTE DESORDENADO AdE1A 36-146 POR SU BLANCO RB" XLIV Reunión Anual de la Sociedad Argentina de Biofísica
POSTER "A maximum entropy two-layer model for codon and amino acid distributions in genomes and proteomes" Workshop “La matemática como herramienta para entender la biología / La biología como fuente de problemas matemáticos”
POSTER "A structure and sequence based model to explain information content relation with growth temperature" Sexto Congreso, Asociación Argentina de Bioinformática y Biología Computacional
TALK "Structural and Energetic Characterization of the Ankyrin Repeat Protein Family"

Sexto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

TALK "Capturing coevolutionary signals in mosaic patterned proteins" Repetitive, Non-Globular Proteins: Nature to Nanotechnology (York)

TALK "Explorando genomas y proteomas mediante modelos de maxima entropia" Workshop "Latin American Conference on Mathematical Modeling of Biological Systems"
TALK "A maximum entropy two-layer model for codon and amino acid distributions in genomes and proteomes" Workshop CELFI “La matemática como herramienta para entender la biología / La biología como fuente de problemas matemáticos”
TALK "PATENA an algorithm for the design of protein linker sequences"

Sexto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

TALK "Convergent evolution and mimicry of protein linear motifs in host- pathogen interactions"

Sexto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

THESIS "Implementación de una herramienta bioinformática para el diseño de secuencias linker"
THESIS Ms.Sc. "Relación estructura-función en Beta-Lactamasas: el rol de la frustración local en las clases A y C" A. Brenda Guzovsky - UBA

2014

PAPER "Frustration in Biomolecules" (Q.Rev. Biophys.) arXiv
PAPER "The E. coli thioredoxin folding mechanism: The key role of the C-terminal helix" Biochimica Biophysica Acta
PAPER "RepeatsDB: A database of tandem repeat protein structures" Nucleic Acids Research
PAPER "Amino acid metabolism conﬂicts with protein diversity" Mol Biol Evol
PAPER "Cysteine-rich positions outside the structural zinc motif of human papillomavirus e7 provide conformational modulation and suggest functional redox roles" Biochemistry
PAPER "The eukaryotic linear motif resource ELM: 10 years and counting" Nucleic Acids Research
POSTER "Periodicities, frustration, energetics and dynamics in the ankyrin repeat fold"

Quinto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

POSTER "Functional modules revealed by combination of enriched domains and linear motifs in ankyrin proteins and their binding partners" ISMB
POSTER "Detecting repetitions and periodicities in proteins by tiling the structural space" Gordon Research Conference on Protein Folding Dynamics
POSTER "A structural view of the ankyrin repeat proteoverse" 1st Symposium on Current Topics in Molecular Biophysics
POSTER "Direct coupling analysis of ankyrin repeat proteins" 1st Symposium on Current Topics in Molecular Biophysics
TALK "Las proteínas son Mosaicos !" Seminarios en la Interfase, Inst Calculo FCEyN-UBA
TALK "Relación estructura función en beta-lactamasas: Clases A y C" 1 E2B2C
TALK "Covariaciones en las secuencias de proteinas repetitivas para la predicción de estructura" AFA

TALK "Amino acid metabolism conflicts with protein diversity"

Quinto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

TALK "Evolution of linear motifs within the adenovirus E1A oncoprotein"

POSTER "Evolution of linear motifs within the adenovirus E1A oncoprotein"

Quinto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

POSTER "Analysis of the Uniprot repertoire of amino acid post translational modifications"

Quinto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

2013

TALK "Análisis e interpretación de estructuras proteicas" SAIC - MDQ
POSTER "STRUCTURE-FUNCTION RELATIONS IN β-LACTAMASES: CLASSES A AND C" 4to Congreso A2B2C
GRANT Conicet/FAPESP "Engineering enzymes for bioethanol production" (rejected)

TALK "Structural Characterization

of the Ankyrin Repeat
Protein Family
"

Cuarto Congreso,

Asociación Argentina de Bioinformática y Biología Computacional

POSTER "What is the information component in sequences of repeat-proteins?" SAB - 2013
TALK "
Repeticiones y Periodicidades: son las proteínas mosaicos estructurales ?

" INGEBI

PAPER "Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space" Journal of Physical Chemistry B
POSTER "Detecting repetitions and periodicities in proteins by tiling the structural space" ISMB - 2013

POSTER "A trade off between energy flux through amino acid metabolism and protein sequence diversity" Latin American Protein Society Meeting

POSTER "Sequence evolution of the intrinsically disordered and globular domains of the adenovirus E1A oncoprotein" Latin American Protein Society Meeting
LECTURE "Viral oncogenesis: reductionist, catastrofist and eco-evolutionary paradigms
" Maestría de Biología Molecular Médica, FCEN-UBA.
PAPER "Folding of a cyclin box: linking multitarget binding to marginal stability, oligomerization and aggregation of the retinoblastoma tumor suppressor AB pocket domain" Journal of Biological Chemistry
PAPER "Minute-timescale prolyl isomerization governs antibody recognition of an intrinsically disordered immunodominant epitope" Journal of Biological Chemistry
GRANT CONICET “Desarrollo de sensores fluorescentes para la medición del hacinamiento molecular en células” (awarded).

2012

PAPER "Protein Frustratometer: a tool to localize the energetic frustration in protein molecules" Nucleic Acids Research
PAPER "Protein stability and dynamics modulation: the case of human frataxin" Plos ONE
TALK "Demitificando el genoma" Semana de la Biología - FCEN - Universidad de Buenos Aires
THESIS Ms.Sc. "Estructura/función en beta-lactamasas: estudio a través de variantes de recombinación" Franco L. Simonetti, UNER
LECTURE "Proteínas: estructura-función-paisajes energéticos-dinámica-frustración" Universidad de Chile
LECTURE "Interacción proteína-ADN" Universidad de Chile

GRANT CONICET-CNRS "From Protein sequence to Function: integrating genomic and molecular dynamics through statistical mechanics" (rejected)
GRANT MINCyT-ECOS "From Protein sequence to Function: integrating genomic and molecular dynamics through statistical mechanics" (rejected)
GRANT Agencia "Del paisaje energético de los polipéptidos a la función biológica de las proteínas:integrando los efectos de perturbaciones locales y globales a la dinámica de plegado deproteínas repetitivas" (awarded)
SCHOLARSHIP CONICET "Papel de las proteínas repetitivas en los procesos de transcripción" (awarded)
TALK"Dissecting relationships among sequence, structures and functions in the ankyrin repeat protein family" Tercer congreso, Asociación Argentina de Bioinformática y Biología Computacional
POSTER "Dissecting relationships between sequence, structure and function in the ankyrin-repeat protein family" ISCB-Latin America

TALK "Could you be more specific, please?" Discusiones informales entre biólogos y matemáticos, FCEN - Universidad de Buenos Aires

PAPER "Evolution of Linear Motifs within the Papillomavirus E7 Oncoprotein
" Journal of Molecular Biology
PAPER "Sequence Evolution of the Intrinsically Disordered and Globular Domains of a Model Viral Oncoprotein" PLoS ONE
GRANT Agencia "Evolución de estructuras, secuencias y funciones en proteínas intrínsecamente desordenadas: motivos LxCxE en oncoproteínas virales
" (awarded)
TALK "Evolution of linear motifs within the papillomavirus E7 oncoprotein
" ISCB-Latin America and Congreso Internacional de Bioinformática y Biología de Sistemas-Costa Rica
TALK "Evolution of linear motifs within intrinsically disordered viral oncoproteins
" Advanced Molecular Biology - EMBL in Argentina, FCEN - Universidad de Buenos Aires
TALK "What is viral oncogenesis?" Protein Physiology Lab, FCEN - Universidad de Buenos Aires
POSTER "Evolution of linear motifs within the intrinsically disordered and globular domains of the papillomavirus E7 oncoprotein" ISCB-Latin America
POSTER "Identification of putative LxCxE motifs targeting the retinoblastoma protein in human viruses by structure and sequence based calculations" ECCB and Tercer congreso, Asociación Argentina de Bioinformática y Biología Computacional
POSTER "Diversity and evolution of retinoblastoma protein-binding LxCxE motifs in human proteins
" Tercer congreso, Asociación Argentina de Bioinformática y Biología Computacional
POSTER "The relation between the divergence of sequence and structure in intrinsically disordered proteins" Tercer congreso, Asociación Argentina de Bioinformática y Biología Computacional
POSTER "LxCxE-motif mediated interaction of viral proteins with the retinoblastoma tumor suppressor a common theme in DNA and RNA virus-host interactions" 3rd ICGEB Workshop on Human RNA viruses

2011

PAPER "The Respiratory Syncytial Virus Transcription Antiterminator M2−1 Is a Highly Stable, Zinc Binding Tetramer with Strong pH-Dependent Dissociation and a Monomeric Unfolding Intermediate" Biochemistry
PAPER "On the role of frustration in the energy landscape of allosteric proteins" Proceedings of the National Academy of Sciences of U.S.A.
PAPER "Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes" Journal of the American Chemical Society
PAPER "Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding" Protein Engineering Design and Selection
GRANT HFSP "Regulating gene networks by engineering intramolecular cooperativity" (rejected)
GRANT HHMI "Frustration and proteins' functional emergence" (rejected)
TALK "Enthalpy-entropy compensation and cooperativity in protein dna complexes" XL reunión, Sociedad Argentina de Biofísica
LECTURE "Epigenética Extrema" Genética Molecular - FCEN - Universidad de Buenos Aires

PAPER "Folding Kinetics of the Cooperatively Folded Subdomain of the IκBα Ankyrin Repeat Domain
" Journal of Molecular Biology
TALK "Repeat proteins: folding in parts, functioning as wholes" 3rd Workshop in Stochasticity in Biochemical reaction networks, BIRS-Banff and XL reunión, Sociedad Argentina de Biofísica
TALK "Paisajes energéticos, plegado y función de proteínas repetitivas" IBYME
POSTER "De la secuencia a la biofísica en proteínas con repeticiones de ankyrina: construcción y análisis de una base de datos" XL reunión, Sociedad Argentina de Biofísica

TALK "Motifmorphosis" Protein Physiology Lab, FCEN - Universidad de Buenos Aires
TALK "Discovery of functional protein linear motifs using a greedy algorithm and information theory" XXXIV Congreso, Sociedad Española de Bioquímica y Biología Molecular
POSTER "Discovery of functional protein linear motifs using a greedy algorithm and information theory" Segundo congreso, Asociación Argentina de Bioinformática y Biología Computacional
THESIS Ms.Sc. "Búsqueda de motivos funcionales en proteínas mediante una heurística Greedy utilizando la Teoría de la Información Molecular" Leandro G. Radusky, FCEN - Universidad de Buenos Aires
LECTURE UBA "Linear motifs in biological sequences studied using molecular information theory" Bioinformática molecular, FCEN - Universidad de Buenos Aires
PAPER "Intrinsic disorder in the human papillomavirus E7 protein" Chapter in Flexible Viruses: Structural disorder within viral proteins
PAPER "Kinetic Recognition of the Retinoblastoma Tumor Suppressor by a Specific Protein Target
" Journal of Molecular Biology
GRANT Agencia "Manipulación de procesos celulares y oncogénesis en infecciones virales persistentes: papel de los motivos LxCxE y PDZ
" (rejected)
GRANT INC "Relaciones genotipo-fenotipo en la oncogénesis viral para proteínas con motivos LxCxE
" (rejected)
TALK "Evolution of linear motifs within the intrinsically disordered and globular domains of the papillomavirus e7 oncoprotein" Institut Pasteur Montevideo and INTA Castelar
POSTER "Structural order and disorder dictate sequence and functional evolution of the papillomavirus E7 protein" Segundo congreso, Asociación Argentina de Bioinformática y Biología Computacional
POSTER "¿Cómo influye el desorden intrínseco en la evolución de la estructura y función de las proteínas?" XL reunión, Sociedad Argentina de Biofísica

2010

PAPER "Experimental snapshots of a protein-DNA binding landscape" Proceedings of the National Academy of Sciences of U.S.A.
GRANT Agencia "Estructura/función en beta-lactamasas: el rol de la frustración local" (awarded)
GRANT Florencio Fiorini "Relaciones Secuencia-Estructura-Función de beta-lactamasas: el rol de la frustración local
" (rejected)
TALK "¿Cuál es la estabilidad relevante de las proteínas?" Primer congreso, Asociación Argentina de Bioinformática y Biología Computacional
TALK "Solvatación nativa en rutas de plegado proteico" IQUIFIB-Universidad de Buenos Aires
TALK "Protein Physiology Lab" Jornadas Departamentales - Departamento de Química Biológica - FCEN - UBA
LECTURE "Proteínas: estructura-función-paisajes energéticos-dinámica-frustración" Estructura y función de macromoléculas - FCEN - Universidad de Buenos Aires

PAPER "Molecular Mechanisms of System Control of NF-kB Signaling by IkBa" Biochemistry
TALK "Paisajes energéticos, plegado y función de proteínas repetitivas" UNeR

GRANT Agencia "Relaciones secuencia-función en motivos lineales de proteínas: estudio mediante la teoría de la información molecular
" (awarded)
TALK "Laboratorio de fisiología de proteínas (2): Ignacio E. Sánchez" Departamento de Química Biológica, FCEN - Universidad de Buenos Aires
TALK "Nacho's research at Laboratorio de fisiología de proteínas" Grupo Interdisciplinario de Biología Estructural, FCEN - Universidad de Buenos Aires

2009

GRANT CONICET "Determinantes del plegado proteico" (awarded)
GRANT Departamento de Química Biológica - FCEN - UBA "Concurso de jefes de grupo de investigación" (awarded)
GRANT Fundación Instituto Leloir "Concurso de jefe del área de bioinformática" (awarded, declined)

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