BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins

Spotorno, Bruno; Piccinini, L.; Tassara, Giovanni; Ruggiero, Carmelina; Nardini, M.; Molina, F.; Rocco, Mattia

doi:10.1007/s002490050095

Cited by 16 publications

(25 citation statements)

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“…32 As we previously suggested, 32 we interpret the experimental ⟨R c 2 ⟩ z data as deriving from the weight-average square cross-sectional radius 33 along the principal axis of the FG main body and of the αC domains. To account for an average molecular mass of ∼320 000 g mol −1 (due to the weak polydispersity of our FG samples 34 ), and considering a theoretical hydration of 0.42 g H 2 O/g FG (calculated by PROMOLP 35 ), an anhydrous diameter d a = 4.1 nm and a density ρ a = 0.875 g cm −3 were employed. The latter is considerably lower than the 1.393 g cm −3 computed from the FG composition, likely reflecting the mostly disordered αC regions being positioned away from the FG main body.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

et al. 2014

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The formation of a fibrin network following fibrinogen enzymatic activation is the central event in blood coagulation and has important biomedical and biotechnological implications. A non-covalent polymerization reaction between macromolecular monomers, it consists basically of two complementary processes: elongation/branching generates an interconnected 3D scaffold of relatively thin fibrils, and cooperative lateral aggregation thickens them more than 10-fold. We have studied the early stages up to the gel point by fast fibrinogen:enzyme mixing experiments using simultaneous small-angle X-ray scattering and wide-angle, multi-angle light scattering detection. The coupled evolutions of the average molecular weight, size, and cross section of the solutes during the fibrils growth phase were thus recovered. They reveal that extended structures, thinner than those predicted by the classic halfstaggered, double-stranded mechanism, must quickly form. Following extensive modeling, an initial phase is proposed in which single-bonded "Y-ladder" polymers rapidly elongate before undergoing a delayed transition to the double-stranded fibrils. Consistent with the data, this alternative mechanism can intrinsically generate frequent, random branching points in each growing fibril. The model predicts that, as a consequence, some branches in these expanding "lumps" eventually interconnect, forming the pervasive 3D network. While still growing, other branches will then undergo a Ca 2+ /length-dependent cooperative collapse on the resulting network scaffolding filaments, explaining their sudden thickening, low final density, and basic mechanical properties.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

et al. 2014

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“…To confirm that these shapes are consistent with the observed hydrodynamic properties, bead models were generated from the atomic coordinates within SNARE complexes (Sutton et al, 1998) by using the program SOMO (Spotorno et al, 1997), and then they were aligned in hypothetical (A) Hydrodynamic information for SNARE complex monomers and dimers was determined experimentally, by using MALLS or AUC as indicated. Predicted molecular weight for a monomeric SNARE complex, including vector-derived amino acids, is 45,768 Da.…”

Section: Global Solution Structure Of Synaptic Snare Complex Multimersmentioning

confidence: 99%

A Role for Soluble N-Ethylmaleimide-sensitive Factor Attachment Protein Receptor Complex Dimerization during Neurosecretion

Fdez

Jowitt

Wang

et al. 2008

MBoC

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The interactions underlying the cooperativity of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes during neurotransmission are not known. Here, we provide a molecular characterization of a dimer formed between the cytoplasmic portions of neuronal SNARE complexes. Dimerization generates a two-winged structure in which the C termini of cytosolic SNARE complexes are in apposition, and it involves residues from the vesicleassociated SNARE synaptobrevin 2 that lie close to the cytosol-membrane interface within the full-length protein.Mutation of these residues reduces stability of dimers formed between SNARE complexes, without affecting the stability of each individual SNARE complex. These mutations also cause a corresponding decrease in the ability of botulinum toxin-resistant synaptobrevin 2 to rescue regulated exocytosis in toxin-treated neuroendocrine cells. Moreover, such synaptobrevin 2 mutants give rise to a dominant-negative inhibition of exocytosis. These data are consistent with an important role for SNARE complex dimers in neurosecretion.

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“…[1] It is based on the ability to realistically calculate the frictional forces and torques experienced by a collection of rigidly connected, arbitrarily placed spheres theoretically immersed in a solvent; importantly, the spheres can be of different radii provided that they do not overlap. [1][2][3][4] The methods employed to represent a macromolecule with beads range from shellmodeling (covering the surface with closely touching small beads, computing their properties, repeating the operation while decreasing the beads size at each iteration, and extrapolating to zero-bead size; see ref. [5] ), to direct correspondence methods (representing selected parts of the macromolecule, such as whole residues or main-chain/ side-chain segments, each with a bead of appropriate volume and position; see ref.…”

Section: Introductionmentioning

confidence: 99%

Developments in the US‐SOMO Bead Modeling Suite: New Features in the Direct Residue‐to‐Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening

Brookes

Demeler

Rocco

2010

Macromolecular Bioscience

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The US-SOMO suite provides a flexible interface for accurately computing solution parameters from 3D structures of biomacromolecules through bead-modeling approaches. We present an extended analysis of the influence of accessible surface area screening, overlap reduction routines, and approximations for non-coded residues and missing atoms on the computed parameters for models built by the residue-to-bead direct correspondence and the cubic grid methods. Importantly, by taking the theoretical hydration into account at the atomic level, the performance of the grid-type models becomes comparable or exceeds that of the corresponding hydrated residue-to-bead models.

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BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins

Cited by 16 publications

References 0 publications

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

A Comprehensive Mechanism of Fibrin Network Formation Involving Early Branching and Delayed Single- to Double-Strand Transition from Coupled Time-Resolved X-ray/Light-Scattering Detection

A Role for Soluble N-Ethylmaleimide-sensitive Factor Attachment Protein Receptor Complex Dimerization during Neurosecretion

Developments in the US‐SOMO Bead Modeling Suite: New Features in the Direct Residue‐to‐Bead Method, Improved Grid Routines, and Influence of Accessible Surface Area Screening

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