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
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
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
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
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
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
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
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
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
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%