Recent Advances in Predicting Functional Impact of Single Amino Acid Polymorphisms: A Review of Useful Features, Computational Methods and Available Tools

2013 ◽  
Vol 8 (2) ◽  
pp. 161-176 ◽  
Author(s):  
Mingjun Wang ◽  
Zhongwei Sun ◽  
Tatsuya Akutsu ◽  
Jiangning Song
Blood ◽  
1991 ◽  
Vol 78 (3) ◽  
pp. 681-687 ◽  
Author(s):  
A Goldberger ◽  
M Kolodziej ◽  
M Poncz ◽  
JS Bennett ◽  
PJ Newman

Abstract The subunits that comprise the platelet-specific integrin alpha IIb beta 3 are polymorphic in nature, with several allelic forms present in the human gene pool. Minor changes in the secondary and tertiary structures of platelet membrane glycoproteins (GP) IIb and IIIa encoded by these alleles can result in an alloimmune reaction after transfusion or during pregnancy. To better understand the molecular structure of the PlA alloantigen system, located on GPIIIa, and the Bak alloantigen on GPIIb, we used a heterologous mammalian expression system to express these integrin subunits in their known polymorphic forms. An expression vector containing the PlA1 form of a GPIIIa cDNA, which encodes a leucine at amino acid 33 (Leu33), was modified to express the PlA2- associated form encoding a proline at amino acid 33 (Pro33). Similarly, a Baka GPIIb cDNA expressing an isoleucine at amino acid 843 (IIe843) was modified to express the Bakb form containing a serine at the same position (Ser843). Transfection of these vectors into COS cells resulted in the synthesis of GPIIb and GPIIIa molecules that were identical in size to those present in platelet lysates. Immunoprecipitation of the GPIIIa-transfected COS lysates with PlA)- specific alloantisera indicated that the Leu33 form was recognized only by anti-PIA1 sera while the Pro33 form was bound only by anti-PlA2 sera, showing that single amino acid polymorphisms are necessary and sufficient to direct the formation of the PlA1 and PlA2 alloepitopes. Similar experiments with Bak allele-specific expression vectors indicated that while the amino acid polymorphism (IIe843 in equilibrium Ser843) was necessary, posttranslational processing of pro-IIb was required for efficient exposure of both the Baka and Bakb alloepitopes.


2014 ◽  
Vol 16 (suppl 5) ◽  
pp. v202-v202
Author(s):  
C. L. Nilsson ◽  
A. Vegvari ◽  
E. Mostovenko ◽  
C. F. Lichti ◽  
D. Fenyo ◽  
...  

2007 ◽  
Vol 05 (06) ◽  
pp. 1215-1231 ◽  
Author(s):  
YUM LINA YIP ◽  
NATHALIE LACHENAL ◽  
VIOLAINE PILLET ◽  
ANNE-LISE VEUTHEY

The UniProt/Swiss-Prot Knowledgebase records about 30,500 variants in 5,664 proteins (Release 52.2). Most of these variants are manually curated single amino acid polymorphisms (SAPs) with references to the literature. In order to keep the list of published documents related to SAPs up to date, an automatic information retrieval method is developed to recover texts mentioning SAPs. The method is based on the use of regular expressions (patterns) and rules for the detection and validation of mutations. When evaluated using a corpus of 9,820 PubMed references, the precision of the retrieval was determined to be 89.5% over all variants. It was also found that the use of nonstandard mutation nomenclature and sequence positional correction is necessary to retrieve a significant number of relevant articles. The method was applied to the 5,664 proteins with variants. This was performed by first submitting a PubMed query to retrieve articles using gene or protein names and a list of mutation-related keywords; the SAP detection procedure was then used to recover relevant documents. The method was found to be efficient in retrieving new references on known polymorphisms. New references on known SAPs will be rendered accessible to the public via the Swiss-Prot variant pages.


PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0137379 ◽  
Author(s):  
Scott H. Millen ◽  
Mineo Watanabe ◽  
Eiji Komatsu ◽  
Fuminori Yamaguchi ◽  
Yuki Nagasawa ◽  
...  

2020 ◽  
Vol 11 ◽  
Author(s):  
Valentina Panzarin ◽  
Argelia Cuenca ◽  
Michele Gastaldelli ◽  
Anna L. F. Alencar ◽  
Francesco Pascoli ◽  
...  

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