scholarly journals Chemical Stabilisation of Collagen as a Biomimetic

2003 ◽  
Vol 3 ◽  
pp. 138-155 ◽  
Author(s):  
R. Gordon Paul ◽  
Allen J. Bailey
Keyword(s):  
The Body ◽  
Collagen Molecule ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Specific Amino Acid ◽  
High Mechanical Strength ◽  
Stable Chemical ◽  
Wide Range ◽  
Recombinant Polypeptides ◽  
Chemical Cross Linking

Collagen is the most abundant protein in animals and because of its high mechanical strength and good resistance to degradation has been utilized in a wide range of products in industry whilst its low antigenicity has resulted in its widespread use in medicine. Collagen products can be purified from fibres, molecules reconstituted as fibres or from specific recombinant polypeptides with preferred properties. A common feature of all these biomaterials is the need for stable chemical cross-linking to control the mechanical properties and the residence time in the body, and to some extent the immunogenicity of the device. This can be achieved by a number of different cross-linking agents that react with specific amino acid residues on the collagen molecule imparting individual biochemical, thermal and mechanical characteristics to the biomaterial. In this review we have summarised the major techniques for testing these characteristics and the mechanisms involved in the variety of cross-linking reactions to achieve particular properties..

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>

scholarly journals Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis

2018 ◽  
Vol 19 (10) ◽  
pp. 2928 ◽  
Author(s):  
Winfried Roseboom ◽  
Madhvi Nazir ◽  
Nils Meiresonne ◽  
Tamimount Mohammadi ◽  
Jolanda Verheul ◽  
...  
Keyword(s):  
Site Directed Mutagenesis ◽  
Cross Linking ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Binding Interface ◽  
Tetrameric Structure ◽  
Z Ring ◽  
Cross Links ◽  
Chemical Cross Linking

Cell division in bacteria is initiated by the polymerization of FtsZ at midcell in a ring-like structure called the Z-ring. ZapA and other proteins assist Z-ring formation and ZapA binds ZapB, which senses the presence of the nucleoids. The FtsZ–ZapA binding interface was analyzed by chemical cross-linking mass spectrometry (CXMS) under in vitro FtsZ-polymerizing conditions in the presence of GTP. Amino acids residue K42 from ZapA was cross-linked to amino acid residues K51 and K66 from FtsZ, close to the interphase between FtsZ molecules in protofilaments. Five different cross-links confirmed the tetrameric structure of ZapA. A number of FtsZ cross-links suggests that its C-terminal domain of 55 residues, thought to be largely disordered, has a limited freedom to move in space. Site-directed mutagenesis of ZapA reveals an interaction site in the globular head of the protein close to K42. Using the information on the cross-links and the mutants that lost the ability to interact with FtsZ, a model of the FtsZ protofilament–ZapA tetramer complex was obtained by information-driven docking with the HADDOCK2.2 webserver.

scholarly journals PTMphinder: an R package for PTM site localization and motif extraction from proteomic datasets

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7046 ◽  
Author(s):  
Jacob M. Wozniak ◽  
David J. Gonzalez
Keyword(s):  
R Package ◽  
Data Sets ◽  
Amino Acid Residues ◽  
Post Translational Modifications ◽  
Specific Amino Acid ◽  
Proteomic Data ◽  
Wide Range ◽  
Site Localization ◽  
Programming Knowledge ◽  
Beta Testing

Background Mass-spectrometry-based proteomics is a prominent field of study that allows for the unbiased quantification of thousands of proteins from a particular sample. A key advantage of these techniques is the ability to detect protein post-translational modifications (PTMs) and localize them to specific amino acid residues. These approaches have led to many significant findings in a wide range of biological disciplines, from developmental biology to cancer and infectious diseases. However, there is a current lack of tools available to connect raw PTM site information to biologically meaningful results in a high-throughput manner. Furthermore, many of the available tools require significant programming knowledge to implement. Results The R package PTMphinder was designed to enable researchers, particularly those with minimal programming background, to thoroughly analyze PTMs in proteomic data sets. The package contains three functions: parseDB, phindPTMs and extractBackground. Together, these functions allow users to reformat proteome databases for easier analysis, localize PTMs within full proteins, extract motifs surrounding the identified sites and create proteome-specific motif backgrounds for statistical purposes. Beta-testing of this R package has demonstrated its simplicity and ease of integration with existing tools. Conclusion PTMphinder empowers researchers to fully analyze and interpret PTMs derived from proteomic data. This package is simple enough for researchers with limited programming experience to understand and implement. The data produced from this package can inform subsequent research by itself and also be used in conjunction with other tools, such as motif-x, for further analysis.

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>

Influence of specific amino acid side-chains on the antimicrobial activity and structure of bovine lactoferrampin1This article is part of Special Issue entitled Lactoferrin and has undergone the Journal’s usual peer review process.

2012 ◽  
Vol 90 (3) ◽  
pp. 362-377 ◽  
Author(s):  
Evan F. Haney ◽  
Kamran Nazmi ◽  
Jan G.M. Bolscher ◽  
Hans J. Vogel
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Peer Review Process ◽  
Titration Calorimetry ◽  
Resonance Spectroscopy ◽  
Bovine Lactoferrin ◽  
Amino Acid Residues ◽  
Scanning Calorimetry ◽  
Specific Amino Acid ◽  
Wide Range

Lactoferrin is an 80 kDa iron binding protein found in the secretory fluids of mammals and it plays a major role in host defence. An antimicrobial peptide, lactoferrampin, was identified through sequence analysis of bovine lactoferrin and its antimicrobial activity against a wide range of bacteria and yeast species is well documented. In the present work, the contribution of specific amino acid residues of lactoferrampin was examined to evaluate the role that they play in membrane binding and bilayer disruption. The structures of all the bovine lactoferrampin derivatives were examined with circular dichroism and nuclear magnetic resonance spectroscopy, and their interactions with phospholipids were evaluated with differential scanning calorimetry and isothermal titration calorimetry techniques. From our results it is apparent that the amphipathic N-terminal helix anchors the peptide to membranes with Trp 268 and Phe 278 playing important roles in determining the strength of the interaction and for inducing peptide folding. In addition, the N-terminal helix capping residues (DLI) increase the affinity for negatively charged vesicles and they mediate the depth of membrane insertion. Finally, the unique flexibility in the cationic C-terminal region of bovine lactoferrampin does not appear to be essential for the antimicrobial activity of the peptide.

scholarly journals Quantitative Cross-Linking of Proteins and Protein

2021 ◽  
pp. 385-400
Author(s):  
Marie Barth ◽  
Carla Schmidt
Keyword(s):  
Mass Spectrometry ◽  
Protein Dynamics ◽  
Structural Changes ◽  
Structural Information ◽  
Protein Complexes ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Wide Range ◽  
Close Proximity ◽  
Cross Links

AbstractCross-linking, in general, involves the covalent linkage of two amino acid residues of proteins or protein complexes in close proximity. Mass spectrometry and computational analysis are then applied to identify the formed linkage and deduce structural information such as distance restraints. Quantitative cross-linking coupled with mass spectrometry is well suited to study protein dynamics and conformations of protein complexes. The quantitative cross-linking workflow described here is based on the application of isotope labelled cross-linkers. Proteins or protein complexes present in different structural states are differentially cross-linked using a “light” and a “heavy” cross-linker. The intensity ratios of cross-links (i.e., light/heavy or heavy/light) indicate structural changes or interactions that are maintained in the different states. These structural insights lead to a better understanding of the function of the proteins or protein complexes investigated. The described workflow is applicable to a wide range of research questions including, for instance, protein dynamics or structural changes upon ligand binding.

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.

Parathyroid gland before and after cisplatin treatment

1987 ◽  
Vol 45 ◽  
pp. 860-861
Author(s):  
S.K. Aggarwal ◽  
J.M. Fadool
Keyword(s):  
Parathyroid Gland ◽  
Wistar Rats ◽  
Antitumor Agent ◽  
The Body ◽  
Cross Linking ◽  
Limiting Factor ◽  
Hormonal Changes ◽  
Primary Mechanism ◽  
Before And After ◽  
Dna Strands

Cisplatin (CDDP) a potent antitumor agent suffers from severe toxic side effects with nephrotoxicity being the major dose-limiting factor, The primary mechanism of its action has been proposed to be through its cross-linking DNA strands. It has also been shown to inactivate various transport enzymes and induce hypocalcemia and hypomagnesemia that may be the underlying cause for some of its toxicities. The present is an effort to study its influence on the parathyroid gland for any hormonal changes that control calcium levels in the body.Male Swiss Wistar rats (Crl: (WI) BR) weighing 200-300 g and of 60 days in age were injected (ip) with cisplatin (7mg/kg in normal saline). The controls received saline injections only. The animals were injected (iv) with calcium (0.5 ml of 10% calcium gluconate/day) and were killed by decapitation on day 1 through 5. Trunk blood was collected in heparinized tubes.

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