Effective estimation of the minimum number of amino acid residues required for functional divergence between duplicate genes

2017 ◽  
Vol 113 ◽  
pp. 126-138 ◽  
Author(s):  
Jingqi Zhou ◽  
Dangyun Liu ◽  
Zhining Sa ◽  
Wei Huang ◽  
Yangyun Zou ◽  
...  
Bionatura ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Ming Ni

Ultra-short peptides are an intrigue new type of biomaterials for various bioapplications. Over the decades, peptides have evolved as biomaterials due to the ease of synthesis, ease of scaling up, feasibility to be functionalized/modified, and recognition by biological system1. Peptide-based hydrogels are widely used as scaffolds for encapsulation and delivery of drugs, genes and cells. They are made of natural amino acids. Thus they are non-immunogenic. They contain carboxylic and amine groups. Thus they can be easily functionalized with bioactive moieties. However, for peptides with more than 16 amino acid residues, they are expensive due to the high synthesis cost. As such, ultra-short peptides with only 2 to 7 amino acid residues stand out due to their easy and cost-effective synthesis, facile assembly in aqueous solution, biocompatibility and mechanical stability. These ultrashort peptides can form hydrogels without the addition of enzymes or other types of cross-linkers.


1987 ◽  
Vol 57 (01) ◽  
pp. 017-019 ◽  
Author(s):  
Magda M W Ulrich ◽  
Berry A M Soute ◽  
L Johan M van Haarlem ◽  
Cees Vermeer

SummaryDecarboxylated osteocalcins were prepared and purified from bovine, chicken, human and monkey bones and assayed for their ability to serve as a substrate for vitamin K-dependent carboxylase from bovine liver. Substantial differences were observed, especially between bovine and monkey d-osteocalcin. Since these substrates differ only in their amino acid residues 3 and 4, it seems that these residues play a role in the recognition of a substrate by hepatic carboxylase.


2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez

<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>


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