COMPUTATIONAL ANALYSIS OF MUTATIONS IN REALLY INTERESTING NEW GENE FINGER DOMAIN AND BRCA1 C TERMINUS DOMAIN OF BREAST CANCER SUSCEPTIBILITY GENE
Abstract
Objective: Breast Cancer 1 (BRCA1), Early Onset and Breast Cancer 2, Early Onset (BRCA2) genes are involved in pathways important for DNA damage
recognition, double-strand break repair, checkpoint control, transcription regulation, and chromatin remodeling. These functions are essential and
important for all cell types. Germline mutations in these genes increase the risk of breast and ovarian cancer in women. In this study, we did an
analysis of the functional and structural impact of all known single nucleotide polymorphisms (SNPs) in BRCA1 and BRCA2 using publicly available
computational prediction tools.
Methods: We analyzed the mutations using two mutation tolerance prediction approaches: Sorting intolerant from tolerant (SIFT), and polymorphism
phenotyping (PolyPhen-2). In addition, stability of the protein was analyzed by I-Mutant. Affinity and stability of really interesting new gene (RING)
and BRCA1 C-terminus (BRCT) domains were also analyzed by BioLuminate tool.
Results: Out of 486 SNPs in BRCA retrieved from functional SNP, a total of 10 SNPs were found to be deleterious by SIFT and PolyPhen. I-Mutant results
indicate that C27F, A1708V could increase the stability of protein, whereas other mutations decrease the stability. Predicted changes in stability and
affinity of RING and BRCT domains of BRCA were computed using residue scanning functionality in bioluminate for all 10 SNPs. The mutation C61R
could affect the stability of RING domain and all mutations in BRCT domain were affecting the inter subunit affinity and stability of the complex.
Conclusion: The combination of computational methods provides a way in understanding the impact of deleterious mutations in altering the BRCA
protein stability and affinity. Based on our investigation, we report potential candidate SNPs for future studies of BRCA mutations.
Keywords: Breast cancer susceptibility gene, BRCA1 C terminus domain, Zinc finger domain, Sorting intolerant from tolerant, Polymorphism
phenotyping, I-mutant, BioLuminate.
Downloads
References
REFERENCES
Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A.
Global cancer statistics, 2012. CA Cancer J Clin 2015;65(2):87-108.
Venkitaraman AR. Linking the cellular functions of BRCA genes to
cancer pathogenesis and treatment. Annu Rev Pathol 2009;4:461-87.
Dever SM, White ER, Hartman MC, Valerie K. BRCA1-directed,
enhanced and aberrant homologous recombination: Mechanism and
potential treatment strategies. Cell Cycle 2012;11(4):687-94.
Christou CM, Kyriacou K. BRCA1 and Its Network of Interacting
Partners. Biology (Basel) 2013;2(1):40-63.
Brzovic PS, Meza JE, King MC, Klevit RE. BRCA1 RING domain
cancer-predisposing mutations. Structural consequences and effects on
protein-protein interactions. J Biol Chem 2001;276(44):41399-406.
Vaux DL, Silke J. IAPs, RINGs and ubiquitylation. Nat Rev Mol Cell
Biol 2005;6(4):287-97.
Lee PH, Shatkay H. An integrative scoring system for ranking SNPs by
their potential deleterious effects. Bioinformatics 2009;25(8):1048-55.
Lee PH, Shatkay H. F-SNP: Computationally predicted functional SNPs
for disease association studies. Nucleic Acids Res 2008;36:D820-4.
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H,
et al. The Protein Data Bank. Nucleic Acids Res 2000;28(1):235-42.
Sahraeian SM, Luo KR, Brenner SE. SIFTER search: A web server for
accurate phylogeny-based protein function prediction. Nucleic Acids
Res 2015;43(W1):W141-7.
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding nonsynonymous
variants on
protein function
using the SIFT
algorithm. Nat
Protoc
;4(7):1073-81.
Ng PC, Henikoff S. Predicting the effects of amino acid substitutions on
protein function. Annu Rev Genomics Hum Genet 2006;7:61-80.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A,
Bork P, et al. A method and server for predicting damaging missense
mutations. Nat Methods 2010;7(4):248-9.
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of
human missense mutations using PolyPhen-2. Current Protocols in
Human Genetics. Unit 7.20. Ch. 7. 2013. DOI:10.1002/0471142905.
hg0720s76.
Bava KA, Gromiha MM, Uedaira H, Kitajima K, Sarai A. ProTherm,
version 4.0: Thermodynamic database for proteins and mutants. Nucleic
Acids Res 2004;32:D120-1.
Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D.
Antibody structure determination using a combination of homology
modeling, energy-based refinement, and loop prediction. Proteins
;82(8):1646-55.
Salam NK, Adzhigirey M, Sherman W, Pearlman DA. Structure-based
approach to the prediction of disulfide bonds in proteins. Protein Eng
Des Sel 2014;27(10):365-74.
Beard H, Cholleti A, Pearlman D, Sherman W, Loving KA. Applying
physics-based scoring to calculate free energies of binding for single
amino acid mutations in protein-protein complexes. PLoS One
;8(12):e82849.
Hashizume R, Fukuda M, Maeda I, Nishikawa H, Oyake D, Yabuki Y,
et al. The RING heterodimer BRCA1-BARD1 is a ubiquitin ligase
inactivated by a breast cancer-derived mutation. J Biol Chem
;276(18):14537-40.
Jin Y, Xu XL, Yang MC, Wei F, Ayi TC, Bowcock AM, et al. Cell cycledependent
colocalization
of BARD1 and
BRCA1 proteins
in discrete
nuclear
domains. Proc Natl Acad
Sci U S A
;941(22):12075-80.
Xia Y, Pao GM, Chen HW, Verma IM, Hunter T. Enhancement of
BRCA1 E3 ubiquitin ligase activity through direct interaction with the
BARD1 protein. J Biol Chem 2003;278(7):5255-63.
Nelson AC, Holt JT. Impact of RING and BRCT domain mutations on
BRCA1 protein stability, localization and recruitment to DNA damage.
Radiat Res 2010;174(1):1-13.
Pace NJ, Weerapana E. Zinc-binding cysteines: Diverse functions and
structural motifs. Biomolecules 2014;4(2):419-34.
Monteiro AN, August A, Hanafusa H. Evidence for a transcriptional
activation function of BRCA1 C-terminal region. Proc Natl Acad Sci U
S A 1996;93(24):13595-9.
Clark SL, Rodriguez AM, Snyder RR, Hankins GD, Boehning D.
Structure-function of the tumor suppressor BRCA1. Comput Struct
Biotechnol J 2012;1(1). pii: e201204005.
Betts MJ, Russell RB. Amino acid properties and consequences of
subsitutions. In: Barnes MR, Gray IC, editors. Bioinformatics for
Geneticists. Chichester, UK: John Wiley & Sons, Ltd.; 2003.
Published
How to Cite
Issue
Section
The publication is licensed under CC By and is open access. Copyright is with author and allowed to retain publishing rights without restrictions.