scholarly journals Symmetric Isostatic Frameworks with $\ell^1$ or $\ell^\infty$ Distance Constraints

10.37236/6044 ◽  
2016 ◽  
Vol 23 (4) ◽  
Author(s):  
Derek Kitson ◽  
Bernd Schulze
Keyword(s):  
Distance Constraints ◽  
Inductive Construction ◽  
Symmetry Operations ◽  
Symmetric Tree

Combinatorial characterisations of minimal rigidity are obtained for symmetric $2$-dimensional bar-joint frameworks with either $\ell^1$ or $\ell^\infty$ distance constraints. The characterisations are expressed in terms of symmetric tree packings and the number of edges fixed by the symmetry operations. The proof uses new Henneberg-type inductive construction schemes.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution

2019 ◽  
Author(s):  
Ricardo N. dos Santos ◽  
F&aacute;bio C. Gozzo ◽  
Faruck Morcos ◽  
Leandro Martinez
Keyword(s):  
Amino Acid ◽  
Chemical Crosslinking ◽  
Distance Constraints

Symmetry-Based Transformable and Foldable Plate Structures

2017 ◽  
Vol 139 (7) ◽  
Author(s):  
Valentina Beatini
Keyword(s):  
The Other ◽  
Rigid Plate ◽  
Plate Structures ◽  
Symmetry Operations

This paper presents a novel family of modular flat-foldable rigid plate structures composed by assemblies of 4R-linkages. First, in the field of foldable plates, the proposed system is characterized by being not only foldable but also transformable: the slope of one module over the other is capable of changing not only magnitude but also sign. This transformable behavior extends the range of application of foldable plates from simply larger–smaller configurations to substantially different configurations and usages. The transformable curve is obtained by means of symmetry operations on the spherical length of links. For each module, three configurations can be designed. Various examples are illustrated.

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