Molecular characterization of novel β-globin variants associated to dominant β-thalassemia

HASENAHUER, MARCIA ANAHÍ; SCHEPS, KAREN GABRIELA; PARISI, GUSTAVO; VARELA, VIVIANA; FORNASARI, MARÍA SILVINA

Bahía Blanca

Congreso; VI Argentinian Conference on Bioinformatics and Computational Biology; 2015

BackgroundThe β-thalassemias (β-thal) (OMIM: 613985) are a group of blood disorders characterized by reduced synthesis of β-globin chains, and hence a diminished production of hemoglobin. We describe here the physicochemical, structural and dynamic characteristics of two novel frameshift mutations in exon 2, which produce elongated chains, and two novel deletions in exons 1 and 2 of the HBB gene, found in three Argentinean and one Paraguayan pediatric patients with dominant β-thalassemia-like features.MethodsThe altered amino acid sequences were studied analyzing their conservation, physicochemical properties, secondary and tertiary structure prediction and Normal Monde Analysis (NMA). PSIPRED [1] was used for protein secondary structure prediction. Intrinsic disorder predictions were done using IUpred program [2]. Tertiary structure modelling was performed using I-Tasser [3] and Robetta [4] programs. The obtained models were energetically evaluated using ProsaWeb [5] and ProCheck[6]. Also, the stabilizing energy contributions of non-covalent interactions between subunits in wild-type oxi and deoxy conformers and for the altered regions were evaluated with computational alanine scanning mutagenesis of protein-protein interfaces using a Robetta routine. In order to evaluate stabilizing interactions that could be affected by the mutations, the iron ion neighborhood was examined for the oxy and deoxy forms. NMA were performed with Bio3D package in R, using wild type and modeled mutants, in order to compare large-scale motions and how they could be affected by the mutations.ConclusionThe novel HBB mutations introduce important variations in charge and could drastically affect the tertiary structure of β-globin as well as their interactions with α-globin. The structural characterization, energetic evaluations and NMA, suggest that the tertiary structure and the positions involved in subunits and heme interactions could be altered in these variants.References1. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 1999;292(2):195-202.2. Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005;21(16):3433-3434.3. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008 Jan 23;9:404. Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004;32(Web Server issue):W526-531.5. Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007;35(Web Server issue):W407-410.6. Laskowski R A, MacArthur M W, Moss D S, Thornton J M. PROCHECK - a program to check the stereochemical quality of protein structures.J. App. Cryst. 1993;26, 283-291.7. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2008, ISBN 3-900051-07-0