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

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 is computed on a single preferably high-resolution structure. Information on system’s dynamics is supplied by ENM-NMA.
The PSN–ENM methodology is made of multiple steps both in the setup and analysis stages, which may discourage inexperienced users. To facilitate its usage, we implemented WebPSN, a freely available web server that allows the user to easily setup the calculation, perform post-processing analyses and both visualize and download numerical and 3D representations of the output. Speed and accuracy make this server suitable to investigate structural communication, including allosterism, in large sets of bio-macromolecular systems.The WebPSN server is freely available at http://webpsn.hpc.unimore.it.

Bioinformatics, 2014, DOI: 10.1093/bioinformatics/btu718

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) was thoroughly investigated by both mathematical modeling of visual phototransduction and atomistic simulations on the major targets of the mutational effect. Mathematical modeling, in line with electrophysiological recordings, indicates reduction of phosphodiesterase 6 (PDE) recognition and activation as the main determinants of the pathological phenotype. Sub-microsecond molecular dynamics (MD) simulations coupled with Functional Mode Analysis improve the resolution of information, showing that such impairment is likely due to disruption of the PDEc binding cavity in transducin. Protein Structure Network analyses additionally suggest that the observed slight reduction of theRGS9-catalyzed GTPase activity of transducin depends on perturbed communication between RGS9 and GTP binding site. These findings provide insights into the structural fundamentals of abnormal functioning of visual phototransduction caused by a missense mutation in one component of the signaling network. This combination of network-centered modeling with atomistic simulations represents a paradigm for future studies aimed at thoroughly deciphering the structural determinants of genetic retinal diseases. Analogous approaches are suitable to unveil the mechanism of information transfer in any signaling network either in physiological or pathological conditions.

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 (ENM)-based strategy, i.e., PSN-ENM, for fast investigation of allosterism in biological systems. PSN analysis and ENM-Normal Mode Analysis (ENM-NMA) are implemented in the structural analysis software Wordom, freely available at http://wordom.sourceforge.net/. The method performs a systematic search of the shortest communication pathways that traverse a protein structure. A number of strategies to compare the structure networks of a protein in different functional states and to get a global picture of communication pathways are presented as well. The approach was validated on the PDZ2 domain from tyrosine phosphatase 1E (PTP1E) in its free (APO) and peptide-bound states. PDZ domains are, indeed, the systems whose structural communication and allosteric features are best characterized both in vitro and in silico. The agreement between predictions by the PSN-ENM method and in vitro evidence is remarkable and comparable to or higher than that reached by more time-consuming computational approaches tested on the same biological system. Finally, the PSN-ENM method was able to reproduce the salient communication features of unbound and bound PTP1E inferred from molecular dynamics simulations. High speed makes this method suitable for high throughput investigation of the communication pathways in large sets of biomolecular systems in different functional states.

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 secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net.

J Comput Chem 32: 1183–1194, 2011  PMID: 21387345

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). For all the considered systems, the intrinsic flexibility of SGDP was higher than that of SGTP, suggesting that Guanine Exchange Factor (GEF) recognition and nucleotide switch require higher amplitude motions than effector recognition or GTP hydrolysis. Functional mode, dynamic domain, and interaction energy correlation analyses highlighted significant differences in the dynamics of small G proteins and Ga proteins, especially in the inactive state. Indeed, SGDP of Gat, is characterized by a more extensive energy coupling between nucleotide binding site and distal regions involved in GEF recognition compared to small G proteins, which attenuates in the active state. Moreover, mechanically distinct domains implicated in nucleotide switch could be detected in the presence of GDP but not in the presence of GTP. Finally, in small G proteins, functional modes are more detectable in the inactive state than in the active one and involve changes in solvent exposure of two highly conserved amino acids in switches I and II involved in GEF recognition. The average solvent exposure of these amino acids correlates in turn with the rate of GDP release, suggesting for them either direct or indirect roles in the process of nucleotide switch. Collectively, nucleotide binding changes the information flow through the conserved Ras-like domain, where GDP enhances the flexibility of mechanically distinct portions involved in nucleotide switch, and favors long distance allosteric communication (in Ga proteins), compared to GTP.

PLoS Comput Biol. 2011 Mar;7(3):e1001098  PMID: 21390270

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 that the hetero- dimeric complexes between the TPa and b isoforms are characterized by contacts between hydrophobic residues in helix 1 from both monomers. Functional characterization confirms that TPa-TPb hetero-dimerization serves to reg- ulate TPa function through agonist-induced internalization, with important implications in cardiovascular homeostasis. The integrated approach employed in this study can be adopted to gain structural and functional insights into the dimerization/oligomerization process of all GPCRs for which the structural model of the monomer can be achieved at reasonable atomic resolution.

Cell. Mol. Life Sci. (2011) 68:3109-3120 PMID: 21213014

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 molecular communication intrinsic to the protein fold. In this study, we predicted likely homodimer architectures of the A2AR and investigated the effects of dimerization on the structure network and the communication paths of the monomeric form. The results of this study emphasize the roles of helix 1 in A2AR dimerization and of highly conserved amino acids in helices 1, 2, 6 and 7 in maintaining the structure network of the A2AR through a persistent hub behavior as well as in the information flow between the extracellular and intracellular poles of the helix bundle. The arginine of the conserved E/DRY motif, R3.50, is not involved in the communication paths but participates in the structure network as a stable hub, being linked to both D3.49 and E6.30 like in the inactive states of rhodopsin. A2AR dimerization affects the communication networks intrinsic to the receptor fold in a way dependent on the dimer architecture. Certain architectures retain the most recurrent communication paths with respect to the monomeric antagonist-bound form but enhancing path numbers and frequencies, whereas some others impair ligand-mediated communication networks. Ligand binding affects the network as well. Overall, the communication network that pertains to the functional dynamics of a GPCR is expected to be influenced by ligand functionality, oligomeric order and architecture of the supramolecular assembly. This article is part of a Special Issue entitled: “Adenosine Receptors”.

Biochimica et Biophysica Acta 1808 (2011) 1256-1266 PMID: 20713020

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 in folding and retinal binding. Rhodopsin fold is charac- terized by networks of amino acids in the retinal and G-protein binding sites likely to play a role in the stability and function of the protein. The distribution of highly connected nodes in the network reflects the existence of a diffuse intramolecular communication inside and between the 2 poles of the helix bundle, which makes pathogenic mutations share similar phe- notypes irrespective of topological and physicochemi- cal differences between them. Because of this commu- nication, the ADRP-linked rhodopsin mutations share a more or less marked ability to impair selected hubs in the protein structure network. The extent of this struc- tural effect relates to the severity of the biochemical defect caused by mutation. The investigative strategy employed in this study is likely to apply to all structur- ally known membrane proteins particularly susceptible to misassembly-causing mutations.

Fanelli, F., Seeber, M. Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants. FASEB J. 24, 3196-3209 (2010). www.fasebj.org

FASEB J. 2010 Sep; 24(9):3196-3209 PMID: 20395457

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 a common function from the protein motions related to functional specialization of selected families or family members. The conserved core is dynamically divided into two lobes. The defor- mation modes, which allow the Ras GTPases to accomplish their switching function, are conserved along evolution and are localized in lobe 1 portions close to the nucleotide. These modes lead to func- tional specialization when associated with evolu- tion-driven deformations of protein portions essen- tially located in lobe 2, distal from the nucleotide, and involved in peculiar interactions with membrane, guanine nucleotide exchange factors, or effectors.

Overall, a complete picture of the functional and evolutionary dynamics of the Ras superfamily emerges.

Structure 18, 402–414, March 10, 2010 PMID: 20223222

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 in the second extracellular loop (EL2) that folds into a twisted β-hairpin were screened through replica exchange molecular dynamics (REMD) simulations using the FACTS implicit solvent model. According to in vitro experiments, ADRP-linked mutants fail to express at the plasma membrane and/or to reconstitute with 11- cis-retinal, indicative of variable defects in protein folding and/or stability. The computational protocol was first probed on the protein G C-terminal β-hairpin, proving the effectiveness of the implicit solvent model in reproducing the free energy landscape of β-hairpin formation. Eight out of the 40 EL2 mutants resulted in misfolding effects on the native β-hairpin structure, consistent with in vitro evidence that they all share severe impairments in folding/expression. Five mutants displayed moderate misfolding attitudes, whereas the remaining 27 mutants, overall characterized by milder effects on rhodopsin expression, did not perturb significantly the conformational behavior of the native β-hairpin but are expected to exert variably disturbing effects on the native interactions of the loop with the chromophore and/or the surrounding receptor domains. Collectively, the results of this study add structural insight to the poorly resolved biochemical behavior of selected class II ADRP mutations, a fundamental step toward an understanding of the atomistic causes of the disease.

Proteins. 2004 Nov 1;57(2):392-9. PMID: 15340926