scholarly journals Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking

2010 ◽  
Vol 78 (16) ◽  
pp. 3409-3427 ◽  
Author(s):  
Stefan Kalkhof ◽  
Sebastian Haehn ◽  
Mats Paulsson ◽  
Neil Smyth ◽  
Jens Meiler ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Disulfide Bonds ◽  
Cross Linking ◽  
Distance Constraints ◽  
Chemical Cross Linking ◽  
Terminal Domains

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>

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>

Biodegradable PEG Hydrogels Cross-linkedUsing Biotin-Avidin Interactions

2010 ◽  
Vol 63 (10) ◽  
pp. 1413 ◽  
Author(s):  
Yingkai Liu ◽  
Jingquan Liu ◽  
Jiangtao Xu ◽  
Shengyu Feng ◽  
Thomas P. Davis
Keyword(s):  
Disulfide Bonds ◽  
Condensation Reaction ◽  
Cross Linking ◽  
Toxic Chemical ◽  
Poly Ethylene Glycol ◽  
Peg Hydrogels ◽  
Pharmaceutical Applications ◽  
The Common ◽  
Poly Ethylene ◽  
Chemical Cross Linking

Poly(ethylene glycol) (PEG) hydrogels are water-swellable, non-toxic, non-immunogenic, and biocompatible. In this paper, we describe the generation of biodegradable PEG hydrogels by cross-linking biotinylated PEG oligomers containing intrinsic disulfide bonds via biotin-avidin interactions. The biotinylated PEG oligomers were synthesized by the condensation reaction between PEG and 3,3′-dithiodipropionic acid, followed by the reaction with biotin. This methodology obviates the need for potentially toxic chemical cross-linking agents that are usually used in the common preparation of hydrogels. Therefore it may be particularly useful in biomedical or pharmaceutical applications.

Structural complementarity of distance constraints obtained from chemical cross‐linking and amino acid coevolution

2019 ◽  
Vol 88 (4) ◽  
pp. 625-632 ◽  
Author(s):  
Ricardo N. Santos ◽  
Guilherme F. Bottino ◽  
Fábio C. Gozzo ◽  
Faruck Morcos ◽  
Leandro Martínez
Keyword(s):  
Amino Acid ◽  
Cross Linking ◽  
Distance Constraints ◽  
Chemical Cross Linking

Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints

2019 ◽  
Vol 35 (17) ◽  
pp. 3005-3012 ◽  
Author(s):  
Allan J R Ferrari ◽  
Fabio C Gozzo ◽  
Leandro Martínez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Structural Modeling ◽  
Supplementary Information ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

Abstract Motivation 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. Results 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. First, the strategy suggests that XL constraints should be set to shorter distances than usually assumed. Second, the complete statistical force-field improves the models obtained and can be easily incorporated into current modeling methods and software. The force-field was implemented and is distributed to be used within the Rosetta ab initio relax protocol. Availability and implementation Force-field parameters and usage instructions are freely available online (http://m3g.iqm.unicamp.br/topolink/xlff). Supplementary information Supplementary data are available at Bioinformatics online.

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