Jessica Andreani

Jessica Andreani
Atomic Energy and Alternative Energies Commission | CEA · Laboratoire de Biologie Structurale et Radiobiologie (LBSR)

PhD

About

50
Publications
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738
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Introduction
Jessica Andreani currently works at the Atomic Energy and Alternative Energies Commission. Jessica does research in Computational Biology and Bioinformatics.

Publications

Publications (50)
Article
Meiotic recombination is triggered by programmed double-strand breaks (DSBs), a subset of these being repaired as crossovers, promoted by eight evolutionarily conserved proteins, named ZMM. Crossover formation is functionally linked to synaptonemal complex (SC) assembly between homologous chromosomes, but the underlying mechanism is unknown. Here w...
Preprint
Full-text available
Meiotic recombination is triggered by programmed double-strand breaks (DSBs), a subset of these being repaired as crossovers, promoted by eight evolutionarily conserved proteins, named ZMM. Crossover formation is functionally linked to synaptonemal complex (SC) assembly between homologous chromosomes, but the underlying mechanism is unknown. Here w...
Article
Full-text available
Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/...
Article
In budding yeast, the MutL homolog heterodimer Mlh1-Mlh3 (MutLγ) plays a central role in the formation of meiotic crossovers. It is also involved in the repair of a subset of mismatches besides the main mismatch repair (MMR) endonuclease Mlh1-Pms1 (MutLα). The heterodimer interface and endonuclease sites of MutLγ and MutLα are located in their C-te...
Article
Full-text available
The InterEvDock3 protein docking server exploits the constraints of evolution by multiple means to generate structural models of protein assemblies. The server takes as input either several sequences or 3D structures of proteins known to interact. It returns a set of 10 consensus candidate complexes, together with interface predictions to guide fur...
Article
Full-text available
Proteo3Dnet is a web server dedicated to the analysis of mass spectrometry interactomics experiments. Given a flat list of proteins, its aim is to organize it in terms of structural interactions to provide a clearer overview of the data. This is achieved using three means: (i) the search for interologs with resolved structure available in the prote...
Article
Motivation: The crucial role of protein interactions and the difficulty in characterising them experimentally strongly motivates the development of computational approaches for structural prediction. Even when protein-protein docking samples correct models, current scoring functions struggle to discriminate them from incorrect decoys. The previous...
Article
Homologous recombination (HR) repairs DNA double-strand breaks using intact homologous sequences as template DNA. Broken DNA and intact homologous sequences form joint molecules (JMs), including Holliday junctions (HJs), as HR intermediates. HJs are resolved to form crossover and noncrossover products. A mismatch repair factor, MLH3 endonuclease pr...
Article
Knowledge of the detailed structure of macromolecular interactions is key to a better understanding and modulation of essential cellular functions and pathological situations. Great efforts are invested in the development of improved computational prediction methods, including binding site prediction and protein–protein docking. These tools should...
Article
Protein–protein interactions play a major role in the molecular machinery of life and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hierarchical view of the interaction...
Article
Full-text available
JIP3 and JIP4 (JNK-interacting proteins 3 and 4) are adaptors for cargo recruitment by dynein/dynactin and kinesin1 motors. Both are dimers that are stabilised by two sections of leucine zipper coiled coils. The N-terminal Leucine Zipper I (LZI) belongs to a section that binds dynein-DLIC and kinesin1-KHC, whilst the medial Leucine Zipper II (LZII)...
Article
Computational structural prediction of macromolecular interactions is a fundamental tool towards the global understanding of cellular processes. The Critical Assessment of PRediction of Interactions (CAPRI) community‐wide experiment provides excellent opportunities for blind testing computational docking methods and includes original targets, thus...
Article
Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design pep...
Article
Full-text available
Kinetochores are macromolecular protein complexes at centromeres that ensure accurate chromosome segregation by attaching chromosomes to spindle microtubules and integrating safeguard mechanisms. The inner kinetochore is assembled on CENP-A nucleosomes and has been implicated in establishing a kinetochore-associated pool of Aurora B kinase, a chrom...
Preprint
Kinetochores are macromolecular protein complexes assembled on centromeric chromatin that ensure accurate chromosome segregation by linking DNA to spindle microtubules and integrating safeguard mechanisms. A kinetochore-associated pool of Ipl1Aurora B kinase, a subunit of the chromosomal passenger complex (CPC), was previously implicated in feedbac...
Article
Full-text available
JIP1 was first identified as scaffold protein for the MAP kinase JNK and is a cargo protein for the kinesin1 molecular motor. JIP1 plays significant and broad roles in neurons, mainly as a regulator of kinesin1-dependent transport, and is associated with human pathologies such as cancer and Alzheimer disease. JIP1 is specifically recruited by the k...
Article
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physi...
Article
Full-text available
Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elus...
Chapter
The structural modeling of protein complexes by docking simulations has been attracting increasing interest with the rise of proteomics and of the number of experimentally identified binary interactions. Structures of unbound partners, either modeled or experimentally determined, can be used as input to sample as extensively as possible all putativ...
Article
Full-text available
Kinesin1 plays a major role in neuronal transport by recruiting many different cargos through its kinesin light chain (KLC). Various structurally unrelated cargos interact with the conserved tetratricopeptide repeat (TPR) domain of KLC. The N-terminal capping helix of the TPR domain exhibits an atypical sequence and structural features that may con...
Data
SEC-MALLS analysis of KLC2-TPR[A1-B6] (A) and KLC1-TPR[A1-B5] (B) fragments. The size-exclusion profiles of the proteins (monitored by refractometry) and the molecular masses (calculated from light-scattering and refractometry data) are plotted. (PDF)
Data
The TPR1:TPR1’ crystal packing contacts. (A) KLC1-TPR[A1-B5] crystal form (this study, pink). The second αA1:αB5’ crystal packing contacts are shown in grey. (B) Superposition of KLC1-TPR[A1-B6] (3NF1, orange) and KLC2-LFPTPR[A1-B6] (5FYJ, green). TPR domain superposition is done on the B1 helix of the main molecule. A1 helices from the main and th...
Data
Crystal packing at the αB5’-sym contact in KLC1-TPR[A1-B5] structure. (A) Details of the interaction between the N-terminal part of the TPR domain (TPR1/2/3 in pink), shown in ribbon, and the C-terminal part of the symmetrical molecule (TPR5 in grey), shown in cartoon. Residues involved in the interface are shown in sticks and hydrogen bonds with d...
Data
Natural and unnatural ligands binding to the N-terminal part of the TPR domain groove of KLC. (A) Superposition of KLC2-TPR[B1-B6]:SKIPWD (3ZFW; red), KLC2-LFPTPR[A1-B6] (5FJY, green), KLC1-TPR[A1-B6] (3NF1, orange) and KLC1-TPR[A1-B5] (this study, purple) on the N-terminal part of the TPR domain. The TPR domain of KLC1-TPR[A1-B6] (3NF1) and KLC1-T...
Article
Netrin-1 is a secreted protein that was first identified 20 years ago as an axon guidance molecule that regulates midline crossing in the CNS. It plays critical roles in various tissues throughout development and is implicated in tumorigenesis and inflammation in adulthood. Despite extensive studies, no inherited human disease has been directly ass...
Article
At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3′-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3′-transition in budding yeast. We find that the 3′-transition globally requires the Pol II elongation factor Spt5 and factors involved...
Article
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. CAPRI (Critical Assessment of PRediction of Interactions) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology developmen...
Article
Full-text available
The structural modeling of protein–protein interactions is key in understanding how cell machineries cross-talk with each other. Molecular docking simulations provide efficient means to explore how two unbound protein structures interact. InterEvDock is a server for protein docking based on a free rigid-body docking strategy. A systematic rigid-bod...
Article
Motivation: It has recently become possible to build reliable de novo models of proteins if a multiple sequence alignment (MSA) of at least 1000 homologous sequences can be built. Methods of global statistical network analysis can explain the observed correlations between columns in the MSA by a small set of directly coupled pairs of columns. Stron...
Article
Protein-protein interactions lie at the heart of most cellular processes. Many experimental and computational studies aim to deepen our understanding of these interactions and improve our capacity to predict them. In this respect, the evolutionary perspective is most interesting, since the preservation of structure and function puts constraints on...
Article
Full-text available
Natural transformation is a major mechanism of horizontal gene transfer in bacteria that depends on DNA recombination. RecA is central to the homologous recombination pathway, catalyzing DNA strand invasion and homology search. DprA was shown to be a key binding partner of RecA acting as a specific mediator for its loading on the incoming exogenous...
Data
Full-text available
Supplementary protocols and figures. Protocols S1–S2 and figures S1–S7. (PDF)
Article
Full-text available
Turnip yellow mosaic virus (TYMV) - a member of the alphavirus-like supergroup of viruses - serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domain (PRO). We recently reported tha...
Article
Full-text available
Motivation: Structural prediction of protein interactions currently remains a challenging but fundamental goal. In particular, progress in scoring functions is critical for the efficient discrimination of near-native interfaces among large sets of decoys. Many functions have been developed using knowledge-based potentials, but few make use of multi...
Data
Full-text available
Supplementary results (sections 1 to 14), materials and methods (sections 15 to 20). (PDF)
Data
Full-text available
Supplementary tables (4 tables) and figures (8 figures). (PDF)
Data
Dataset describing all 1,024 pairs of interologs used in this study, as well as all 387 pairs of complexes in the redundant95 dataset. This dataset contains information such as interface sequence identity, structure resolution, interface RMSD, as well as the non-obligate or obligate nature of the interfaces, the likely paralogs and orthologs among...
Conference Paper
Full-text available
Helicobacter pylori, the only bacterial pathogen classified as a human carcinogen by the WHO, displays an amazing genetic variability. The molecular mechanisms underlying its genomic plasticity have being partially assigned to error-prone DNA repair systems, to high levels of DNA replication errors and to efficient homologous or homeologous recombi...
Article
Full-text available
Evolutionary pressures act on protein complex interfaces so that they preserve their complementarity. Nonetheless, the elementary interactions which compose the interface are highly versatile throughout evolution. Understanding and characterizing interface plasticity across evolution is a fundamental issue which could provide new insights into prot...
Article
Full-text available
Capturing how the structures of interacting partners evolved at their binding interfaces is a fundamental issue for understanding interactomes evolution. In that scope, the InterEvol database was designed for exploring 3D structures of homologous interfaces of protein complexes. For every chain forming a complex in the protein data bank (PDB), clos...

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