scholarly journals Site-Specific Amino Acid Replacement Matrices from Structurally Constrained Protein Evolution Simulations

2002 ◽  
Vol 19 (3) ◽  
pp. 352-356 ◽  
Author(s):  
María Silvina Fornasari ◽  
Gustavo Parisi ◽  
Julian Echave
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Amino Acid Replacement ◽  
Site Specific ◽  
Specific Amino Acid

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 445-458 ◽  
Author(s):  
Nick Goldman ◽  
Jeffrey L Thorne ◽  
David T Jones
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Protein Evolution ◽  
Solvent Accessibility ◽  
Strong Association ◽  
Length Distribution ◽  
Parametric Bootstrap ◽  
Amino Acid Replacement ◽  
Physical Constraints ◽  
The Impact

Abstract Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.

scholarly journals Site-specific amino acid alterations in Ca2+ binding domains in calmodulin impair activation of RBC Ca(2+)-ATPase

1992 ◽  
Vol 62 (1) ◽  
pp. 77-78 ◽  
Author(s):  
D. Kosk-Kosicka ◽  
T. Bzdega ◽  
A. Wawrzynow ◽  
D.M. Watterson ◽  
T.J. Lukas
Keyword(s):  
Amino Acid ◽  
Site Specific ◽  
Specific Amino Acid ◽  
Binding Domains

scholarly journals Prediction of Site-Specific Amino Acid Distributions and Limits of Divergent Evolutionary Changes in Protein Sequences

2004 ◽  
Vol 22 (3) ◽  
pp. 630-638 ◽  
Author(s):  
Markus Porto ◽  
H. Eduardo Roman ◽  
Michele Vendruscolo ◽  
Ugo Bastolla
Keyword(s):  
Amino Acid ◽  
Protein Sequences ◽  
Site Specific ◽  
Specific Amino Acid ◽  
Evolutionary Changes

scholarly journals Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs

2015 ◽  
Author(s):  
Michael B Doud ◽  
Orr Ashenberg ◽  
Jesse Bloom
Keyword(s):  
Amino Acid ◽  
Molecular Phylogenetics ◽  
Amino Acid Identity ◽  
Comparative Sequence Analysis ◽  
Influenza Viruses ◽  
Evolutionary Modeling ◽  
Homologous Proteins ◽  
Site Specific ◽  
Specific Amino Acid ◽  
Limited Change

Evolution drives changes in a protein's sequence over time. The extent to which these changes in sequence lead to shifts in the underlying preference for each amino acid at each site is an important question with implications for comparative sequence-analysis methods such as molecular phylogenetics. To quantify the extent that site-specific amino-acid preferences shift during evolution, we performed deep mutational scanning on two homologs of human influenza nucleoprotein with 94% amino-acid identity. We found that only a modest fraction of sites exhibited shifts in amino-acid preferences that exceeded the noise in our experiments. Furthermore, even among sites that did exhibit detectable shifts, the magnitude tended to be small relative to differences between non-homologous proteins. Given the limited change in amino-acid preferences between these close homologs, we tested whether our measurements could inform site-specific substitution models that describe the evolution of nucleoproteins from more diverse influenza viruses. We found that site-specific evolutionary models informed by our experiments greatly outperformed non-site-specific alternatives in fitting phylogenies of nucleoproteins from human, swine, equine, and avian influenza. Combining the experimental data from both homologs improved phylogenetic fit, partly because measurements in multiple genetic contexts better captured the evolutionary average of the amino-acid preferences for sites with shifting preferences. Our results show that site-specific amino-acid preferences are sufficiently conserved that measuring mutational effects in one protein provides information that can improve quantitative evolutionary modeling of nearby homologs.

scholarly journals Bioconjugates of Intelligent Polymers and Recognition Proteins for Use in Diagnostics and Affinity Separations

2000 ◽  
Vol 46 (9) ◽  
pp. 1478-1486 ◽  
Author(s):  
Allan S Hoffman
Keyword(s):  
Amino Acid ◽  
Protein A ◽  
Acid Sites ◽  
Genetically Engineered ◽  
Smart Polymers ◽  
Amino Groups ◽  
Site Specific ◽  
Specific Amino Acid ◽  
Random Polymer ◽  
Intelligent Polymers

Abstract Polymers that respond to small changes in environmental stimuli with large, sometimes discontinuous changes in their physical state or properties are often called “intelligent” or “smart” polymers. We have conjugated these polymers to different recognition proteins, including antibodies, protein A, streptavidin, and enzymes. These bioconjugates have been prepared by random polymer conjugation to lysine amino groups on the protein surface, and also by site-specific conjugation of the polymer to specific amino acid sites, such as cysteine sulfhydryl groups, that are genetically engineered into the known amino acid sequence of the protein. We have conjugated several different smart polymers to streptavidin, including temperature-, pH-, and light-sensitive polymers. The preparation of these conjugates and their many fascinating applications are reviewed here.

scholarly journals Probing Structural Features of Alzheimer’s Amyloid-β Pores in Bilayers Using Site-Specific Amino Acid Substitutions

Biochemistry ◽  
2012 ◽  
Vol 51 (3) ◽  
pp. 776-785 ◽  
Author(s):  
Ricardo Capone ◽  
Hyunbum Jang ◽  
Samuel A. Kotler ◽  
Bruce L. Kagan ◽  
Ruth Nussinov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amyloid Β ◽  
Structural Features ◽  
Amino Acid Substitutions ◽  
Site Specific ◽  
Specific Amino Acid
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