WebPSN: a web server for high-throughput investigation of structural communication in bio-macromolecules

WebPSN: a web server for high-throughput investigation of structural communication in bio-macromolecules

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study

A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study

Software News and Updates Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces

Software News and Updates Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces

Nucleotide Binding Switches the Information Flow in Ras GTPases

Nucleotide Binding Switches the Information Flow in Ras GTPases

Light on the structure of thromboxane A2 receptor heterodimers

Light on the structure of thromboxane A2 receptor heterodimers

Dimerization and ligand binding affect the structure network of A2A adenosine receptor

Dimerization and ligand binding affect the structure network of A2A adenosine receptor

Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants

Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily – Structure, 2010

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily – Structure, 2010

Computational Screening of Rhodopsin Mutations Associated with Retinitis Pigmentosa

Computational Screening of Rhodopsin Mutations Associated with Retinitis Pigmentosa

michele seeber

WebPSN: a web server for high-throughput investigation of structural communication in bio-macromolecules

WebPSN: a web server for high-throughput investigation of structural communication in bio-macromolecules

Michele Seeber, Angelo Felline, Francesco Raimoni, Simona Mariani, and Francesca Fanelli We developed a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy (i.e. PSN-ENM) to investigate structural communication in biomacromolecules. The approach starts from a Protein Structure Graph and searches for all shortest communication pathways between user-specified residues. The graph […]

Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases

Simona Mariani, Daniele Dell’Orco, Angelo Felline, Francesco Raimondi,¬† and Francesca Fanelli A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction. Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations. The transducin G38D mutant associated with the Nougaret Congenital Night Blindness (NCNB) […]

A Mixed Protein Structure Network and Elastic Network Model Approach to Predict the Structural Communication in Biomolecular Systems: The PDZ2 Domain from Tyrosine Phosphatase 1E As a Case Study

Francesco Raimondi, Angelo Felline, Michele Seeber, Simona Mariani, and Francesca Fanelli ABSTRACT: Graph theory is being increasingly used to study the structural communication in biomolecular systems. This requires incorporating information on the system’s dynamics, which is time-consuming and not suitable for high-throughput investigations. We propose a mixed Protein Structure Network (PSN) and Elastic Network Model […]

Software News and Updates Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces

MICHELE SEEBER, ANGELO FELLINE, FRANCESCO RAIMONDI, STEFANIE MUFF, RAN FRIEDMAN, FRANCESCO RAO, AMEDEO CAFLISCH, FRANCESCA FANELLI Abstract: Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular struc- tures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of […]

Nucleotide Binding Switches the Information Flow in Ras GTPases

Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli Abstract The Ras superfamily comprises many guanine nucleotide-binding proteins (G proteins) that are essential to intracellular signal transduction. The guanine nucleotide-dependent intrinsic flexibility patterns of five G proteins were investigated in atomic detail through Molecular Dynamics simulations of the GDP- and GTP-bound states (SGDP and SGTP, respectively). […]

Light on the structure of thromboxane A2 receptor heterodimers

Francesca Fanelli, Mario Mauri, Valerie Capra, Francesco Raimondi, ¬†Francesca Guzzi, Manuela Ambrosio, G. Enrico Rovati and Marco Parenti Abstract The structure-based design of a mutant form of the thromboxane A2 prostanoid receptor (TP) was instru- mental in characterizing the structural determinants of the hetero-dimerization process of this G protein coupled receptor (GPCR). The results suggest […]

Dimerization and ligand binding affect the structure network of A2A adenosine receptor

Francesca Fanelli, Angelo Felline Abstract G protein Coupled Receptors (GPCRs) are allosteric proteins whose functioning fundamentals are the communication between the two poles of the helix bundle. The representation of GPCR structures as networks of interacting amino acids can be a meaningful way to decipher the impact of ligand and of dimerization/ oligomerization on the […]

Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants

Francesca Fanelli and Michele Seeber ABSTRACT Disease-causing missense mutations in membrane proteins, such as rhodopsin mutations asso- ciated with the autosomal dominant form of retinitis pigmentosa (ADRP), are often linked to defects in folding and/or trafficking. The mechanical unfolding of wild-type rhodopsin was compared with that of 20 selected ADRP-linked mutants more or less defective […]

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily – Structure, 2010

Francesco Raimondi, Modesto Orozco, and Francesca Fanelli SUMMARY The evolutionary and physical deformability patterns of members of the Ras GTPase superfamily were investigated by Principal Component and Elastic Network-Normal Mode analyses. The study helped to decipher the dynamics infor- mation encrypted into the conserved core and to separate the trans-family intrinsic flexibility associ- ated with […]

Computational Screening of Rhodopsin Mutations Associated with Retinitis Pigmentosa

Angelo Felline, Michele Seeber, Francesco Rao, and Francesca Fanelli   Abstract: Retinitis pigmentosa (RP) refers to a group of debilitating, hereditary disorders that cause severe visual impairment in as many as 1.5 million patients worldwide. Rhodopsin mutations account for >25% of the autosomal dominant form of the disease (ADRP). Forty artificial and ADRP-associated mutations located […]