Amino Acids

, Volume 43, Issue 2, pp 603–615

In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein

  • Vidya Rajendran
  • Rituraj Purohit
  • Rao Sethumadhavan
Original Article


Lamin A/C proteins are the major components of a thin proteinaceous filamentous meshwork, the lamina, that underlies the inner nuclear membrane. A few specific mutations in the lamin A/C gene cause a disease with remarkably different clinical features: FPLD, or familial partial lipodystrophy (Dunnigan-type), which mainly affects adipose tissue. Lamin A/C mutant R482W is the key variant that causes FPLD. Biomolecular interaction and molecular dynamics (MD) simulation analysis were performed to understand dynamic behavior of native and mutant structures at atomic level. Mutant lamin A/C (R482W) showed more interaction with its biological partners due to its expansion of interaction surface and flexible nature of binding residues than native lamin A/C. MD simulation clearly indicates that the flexibility of interacting residues of mutant are mainly due to less involvement in formation of inter and intramolecular hydrogen bonds. Our analysis of native and Mutant lamin A/C clearly shows that the structural and functional consequences of the mutation R482W causes FPLD. Because of the pivotal role of lamin A/C in maintaining dynamics of nuclear function, these differences likely contribute to or represent novel mechanisms in laminopathy development.


Docking simulation Laminopathy RMSD SASA 


  1. Amadei A, Linssen ABM, Berendsen HJC (1993) Essential dynamics of proteins. Proteins 17:412–425PubMedCrossRefGoogle Scholar
  2. Araújo-Vilar D, Lattanzi G, González-Méndez B, Costa-Freitas AT, Prieto D, Columbaro M, Mattioli E, Victoria B, Martínez-Sánchez N, Ramazanova A, Fraga M, Beiras A, Forteza J, Domínguez-Gerpe L, Calvo C, Lado-Abeal J (2009) Site-dependent differences in both prelamin A and adipogenic genes in subcutaneous adipose tissue of patients with type 2 familial partial lipodystrophy. J Med Genet 46(1):40–48PubMedCrossRefGoogle Scholar
  3. Bank EM, Ben-Harush K, Wiesel-Motiuk N, Barkan R, Feinstein N, Lotan O, Medalia O, Gruenbaum Y (2011) A laminopathic mutation disrupting lamin filament assembly causes disease-like phenotypes in Caenorhabditis elegans. Mol Biol Cell 22(15):2716–2728PubMedCrossRefGoogle Scholar
  4. Berendsen HJC, Postma JPM, Gunsteren WFV, Hermans J (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. D Reidel Publishing Company, Dordrecht, pp 331–342Google Scholar
  5. Berendsen HJC, Postma JPM, DiNola A, Hakk JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  6. Berman HM, Westbrook JZ, Feng G, Gilliland TN, Bhat H, Weissig IN et al (2000) Nucleic Acids Res 28:235–242PubMedCrossRefGoogle Scholar
  7. Bione S, Maestrini E, Rivella S, Mancini M, Regis S, Romeo G, Toniolo D (1994) Identification of a novel X-linked gene responsible for Emery–Dreifuss muscular dystrophy. Nat Genet 8:323–327PubMedCrossRefGoogle Scholar
  8. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921PubMedCrossRefGoogle Scholar
  9. Burke B, Stewart CL (2002) Life at the edge: the nuclear envelope and human disease. Nat Rev Mol Cell Biol 3:575–585PubMedCrossRefGoogle Scholar
  10. Burn J, Baraitser M (1986) Partial lipoatrophy with insulin resistant diabetes and hyperlipidaemia (Dunnigan syndrome). J Med Genet 23:128–130PubMedCrossRefGoogle Scholar
  11. Cao H, Hegele RA (2000) Nuclear lamin A/C R482Q mutation in Canadian kindreds with Dunnigan-type familial partial lipodystrophy. Hum Mol Genet 9:109–112PubMedCrossRefGoogle Scholar
  12. Case DA, Pearlman DA, Caldwell JW, Wang J, Ross WS, Simmerling CL, Darden TA, Mertz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsue V, Gohlke H, Radmer R, Duan Y, Pitera J, Massova I, Seibel GL, Singh C, Weiner P, Kollman PA (2002) AMBER simulation software package, version 7, vol 2006. University of California, San FranciscoGoogle Scholar
  13. Clements L, Manilal S, Love DR, Morris GE (2000) Direct interaction between emerin and lamin A. Biochem Biophys Res Commun 267:709–714PubMedCrossRefGoogle Scholar
  14. Cohen M, Lee KK, Wilson KL, Gruenbaum Y (2001) Transcriptional repression, apoptosis, human disease and the functional evolution of the nuclear lamina. Trends Biochem Sci 26:41–47PubMedCrossRefGoogle Scholar
  15. de Vries SJ, van Dijk M, Bonvin AMJJ (2010) The HADDOCK web server for data-driven biomolecular docking. Nat Protoc 5:883–897PubMedCrossRefGoogle Scholar
  16. Dhe-Paganon S, Werner ED, Chi YI, Shoelson SE (2002) Structure of the globular tail of nuclear lamin. J Biol Chem 277(20):17381–17384PubMedCrossRefGoogle Scholar
  17. Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737PubMedCrossRefGoogle Scholar
  18. Eisenhaber F, Argos P (1996) Hydrophobic regions on protein surfaces: definition based on hydration shell structure and a quick method for their computation. Protein Eng 9(12):1121–1133PubMedCrossRefGoogle Scholar
  19. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr Sect D Biol Crystallogr 60:2126–2132CrossRefGoogle Scholar
  20. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593CrossRefGoogle Scholar
  21. Frock RL, Kudlow BA, Evans AM, Jameson SA, Hauschka SD, Kennedy BK (2006) Lamin A/C and emerin are critical for skeletal muscle satellite cell differentiation. Genes Dev 20(4):486–500PubMedCrossRefGoogle Scholar
  22. Garg A, Peshock RM, Fleckenstein JL (1999) Adipose tissue distribution pattern in patients with familial partial lipodystrophy (Dunnigan variety). J Clin Endocrinol Metab 84:170–174PubMedCrossRefGoogle Scholar
  23. Gunsteren WFV, Billeter SR, Eising AA, Hunenberger PH, Kruger P, Mark AE, Scott WRP, Tironi TG (1996) Biomolecular simulation: the Gromos 96 manual and user guide. Hochschulverlag AG an der Zurich, ZurichGoogle Scholar
  24. Halperin I, Ma B, Wolfson H, Nussinov R (2002) Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins Struct Funct Genet 47:409–443PubMedCrossRefGoogle Scholar
  25. Hegele RA (2001) Premature atherosclerosis associated with monogenic insulin resistance. Circulation 103:2225–2229PubMedCrossRefGoogle Scholar
  26. Hegele RA, Cao H, Anderson CM, Hramiak IM (2000a) Heterogeneity of nuclear lamin A mutations in Dunnigan-type familial partial lipodystrophy. J Clin Endocrinol Metab 85:3431–3435PubMedCrossRefGoogle Scholar
  27. Hegele RA, Anderson CM, Cao H (2000b) Lamin A/C mutation in a woman and her two daughters with Dunnigan-type partial lipodystrophy and insulin resistance. Diabetes Care 23:258–259PubMedCrossRefGoogle Scholar
  28. Hess B, Kutzner C, Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447CrossRefGoogle Scholar
  29. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33–38PubMedCrossRefGoogle Scholar
  30. Jacob KN, Garg A (2006) Laminopathies: multisystem dystrophy syndromes. Mol Genet Metab 87:289–302PubMedCrossRefGoogle Scholar
  31. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ (2003) CAPRI: a critical assessment of predicted interactions. Proteins Struct Funct Genet 52:2–9PubMedCrossRefGoogle Scholar
  32. Kim JB, Spiegelman BM (1996) ADD1/SREBP1 promotes adipocyte differentiation and gene expression linked to fatty acid metabolism. Genes Dev 10(9):1096–1107PubMedCrossRefGoogle Scholar
  33. Kobberling J, Dunnigan MF (1986) Familial partial lipodystrophy: two types of an X linked dominant syndrome, lethal in the hemizygous state. J Med Genet 23:120–127PubMedCrossRefGoogle Scholar
  34. Lado-Abeal J, Calvo RM, Victoria B, Castro I, Obregon MJ, Araujo-Vilar D (2010) Regional decrease of subcutaneous adipose tissue in patients with type 2 familial partial lipodystrophy is associated with changes in thyroid hormone metabolism. Thyroid. 20(4):419–424PubMedCrossRefGoogle Scholar
  35. Lloyd DJ, Trembath RC, Shackleton S (2002) A novel interaction between lamin A and SREBP1: implications for partial lipodystrophy and other laminopathies. Hum Mol Genet 11:769–777PubMedCrossRefGoogle Scholar
  36. Magracheva E, Kozlov S, Stewart CL, Wlodawer A, Zdanov A (2009) Structure of the lamin A/C R482W mutant responsible for dominant familial partial lipodystrophy (FPLD). Acta Crystallogr Sect F Struct Biol Cryst Commun 65:665–670PubMedCrossRefGoogle Scholar
  37. Manilal S, Man NT, Morris GE (1998) Colocalization of emerin and lamins in interphase nuclei and changes during mitosis. Biochem Biophys Res Commun 249:643–647PubMedCrossRefGoogle Scholar
  38. Manilal S, Sewry CA, Pereboev A (1999) Colocalization of emerin and lamins in interphase nuclei and changes during mitosis. Hum Mol Genet 8:353–359PubMedCrossRefGoogle Scholar
  39. Maraldi NM, Capanni C, Mattioli E, Columbaro M, Squarzoni S, Parnaik WK, Wehnert M, Lattanzi G (2007) A pathogenic mechanism leading to partial lipodystrophy and prospects for pharmacological treatment of insulin resistance syndrome. Acta Biomed 78:207–215PubMedGoogle Scholar
  40. Maraldi NM, Capanni C, Cenni V, Fini M, Lattanzi G (2011) Laminopathies and lamin-associated signaling pathways. J Cell Biochem 112(4):979–992PubMedCrossRefGoogle Scholar
  41. McDonald IK, Thornton JM (1994) Satisfying hydrogen bonding potential in proteins. J Mol Biol 238:777–793PubMedCrossRefGoogle Scholar
  42. Newport JW, Wilson KL, Dunphy WG (1990) A lamin-independent pathway for nuclear envelope assembly. J Cell Biol 111:2247–2259PubMedCrossRefGoogle Scholar
  43. Nikolova V, Leimena C, McMahon AC, Tan JC, Chandar S, Jogia D, Kesteven SH, Michalicek J, Otway R, Verheyen F, Rainer S, Stewart CL, Martin D, Feneley MP, Fatkin D (2004) Defects in nuclear structure and function promote dilated cardiomyopathy in lamin A/C-deficient mice. J Clin Invest 113(3):357–369PubMedGoogle Scholar
  44. Nilges M (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 245:645–660PubMedCrossRefGoogle Scholar
  45. Nilges M, Macias MJ, O’Donoghue SI, Oschkinat H (1997) Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol 269:408–422PubMedCrossRefGoogle Scholar
  46. Ostlund C, Ellenberg J, Hallberg E, Lippincott-Schwartz J, Worman HJ (1999) Intracellular trafficking of emerin, the Emery–Dreifuss muscular dystrophy protein. J Cell Sci 112:1709–1719PubMedGoogle Scholar
  47. Ostlund C, Bonne G, Schwartz K, Worman HJ (2001) Properties of lamin A mutants found in Emery–Dreifuss muscular dystrophy, cardiomyopathy and Dunnigan-type partial lipodystrophy. J Cell Sci 114:4435–4445PubMedGoogle Scholar
  48. Párraga A, Bellsolell L, Ferré-D’Amaré AR, Burley SK (1998) Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution. Structure 6(5):661–672PubMedCrossRefGoogle Scholar
  49. Prokocimer M, Davidovich M, Nissim-Rafinia M, Wiesel-Motiuk N, Bar DZ, Barkan R, Meshorer E, Gruenbaum Y (2009) Nuclear lamins: key regulators of nuclear structure and activities. J Cell Mol Med 13:1059–1085PubMedCrossRefGoogle Scholar
  50. Purohit R, Sethumadhavan R (2009) Structural Basis for the resilience of darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdiscip Sci 1(4):320–328PubMedCrossRefGoogle Scholar
  51. Purohit R, Rajasekaran R, Sudandiradoss C, George Priya Doss C, Ramanathan K, Sethumadhavan R (2008) Studies on flexibility and binding affinity of Asp25 of HIV-1 protease mutants. Int J Biol Macromol 42(4):386–391PubMedCrossRefGoogle Scholar
  52. Purohit R, Rajendran V, Sethumadhavan R (2011a) Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and isoniazid susceptibility: an in silico analysis. J Mol Model 17(4):869–877PubMedCrossRefGoogle Scholar
  53. Purohit R, Rajendran V, Sethumadhavan R (2011b) Studies on adaptability of binding residues and flap region of TMC-114 resistance HIV-1 protease mutants. J Biomol Struct Dyn 29(1):137–152PubMedCrossRefGoogle Scholar
  54. Sakaki M, Koike H, Takahashi N, Sasagawa N, Tomioka S, Arahata K, Ishiura S (2001) Interaction between emerin and nuclear lamins. J Biochem 129(2):321–327PubMedCrossRefGoogle Scholar
  55. Schmidt HH, Genschel J, Baier P, Schmidt M, Ockenga J, Tietge UJ, Pröpsting M, Büttner C, Manns MP, Lochs H, Brabant G (2001) Dyslipemia in familial partial lipodystrophy caused by an R482W mutation in the LMNA gene. J Clin Endocrinol Metab 86(5):2289–2295PubMedCrossRefGoogle Scholar
  56. Shackleton S, Lloyd DJ, Jackson SN, Evans R, Niermeijer MF, Singh BM, Schmidt H, Brabant G, Kumar S, Durrington PN, Gregory S, O’Rahilly S, Trembath RC (2000) LMNA, encoding lamin A/C, is mutated in partial lipodystrophy. Nat Genet 24:153–156PubMedCrossRefGoogle Scholar
  57. Speckman RA, Garg A, Du F, Bennett L, Veile R, Arioglu E, Taylor SI, Lovett M, Bowcock AM (2000) Mutational and haplotype analyses of families with familial partial lipodystrophy (Dunnigan variety) reveal recurrent missense mutations in the globular C-terminal domain of lamin A/C. Am J Hum Genet 66:1192–1198PubMedCrossRefGoogle Scholar
  58. Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718CrossRefGoogle Scholar
  59. Strelkov SV, Herrmann H, Aebi U (2003) Molecular architecture of intermediate filaments. Bioessays 25:243–251PubMedCrossRefGoogle Scholar
  60. Stuurman N, Heins S, Aebi U (1998) Nuclear lamins: their structure, assembly, and interactions. J Struct Biol 122:42–66PubMedCrossRefGoogle Scholar
  61. Sullivan T, Escalante-Alcalde D, Bhatt H, Anver M, Bhat N, Nagashima K, Stewart CL, Burke B (1999) Loss of A-type lamin expression compromises nuclear envelope integrity leading to muscular dystrophy. J Cell Biol 147:913–920PubMedCrossRefGoogle Scholar
  62. Teng S, Madej T, Panchenko A, Alexov E (2009) Modeling effects of human single nucleotide polymorphisms on protein–protein interactions. Biophys J 96(6):2178–2188PubMedCrossRefGoogle Scholar
  63. Tilgner K, Wojciechowicz K, Jahoda C, Hutchison C, Markiewicz E (2009) Dynamic complexes of A-type lamins and emerin influence adipogenic capacity of the cell via nucleocytoplasmic distribution of {beta}-catenin. J Cell Sci 122:401–413PubMedCrossRefGoogle Scholar
  64. Tsuchiya Y, Hase A, Ogawa M, Yorifuji H, Arahata A (1999) Distinct regions specify the nuclear membrane targeting of emerin, the responsible protein for Emery–Dreifuss muscular dystrophy. Eur J Biochem 259:859–886PubMedCrossRefGoogle Scholar
  65. Vallone B, Miele AE, Vecchini P, Chiancone E, Brunori M (1998) Free energy of burying hydrophobic residues in the interface between protein subunits. Proc Natl Acad Sci USA 95:6103–6107PubMedCrossRefGoogle Scholar
  66. Vantyghem MC, Pigny P, Maurage CA, Rouaix-Emery N, Stojkovic T, Cuisset JM, Millaire A, Lascols O, Vermersch P, Wemeau JL, Capeau J, Vigouroux C (2004) Patients with familial partial lipodystrophy of the Dunnigan type due to a LMNA R482W mutation show muscular and cardiac abnormalities. J Clin Endocrinol Metab 89(11):5337–5346PubMedCrossRefGoogle Scholar
  67. Vantyghem MC, Faivre-Defrance F, Marcelli-Tourvieille S, Fermon C, Evrard A, Bourdelle-Hego MF (2007) Familial partial lipodystrophy due to the LMNA R482W mutation with multinodular goitre, extrapyramidal syndrome and primary hyperaldosteronism. Clin Endocrinol (Oxf) 67(2):247–249CrossRefGoogle Scholar
  68. Vigouroux C, Magré J, Vantyghem MC, Bourut C, Lascols O, Shackleton S, Lloyd DJ, Guerci B, Padova G, Valensi P, Grimaldi A, Piquemal R, Touraine P, Trembath RC, Capeau J (2000) Lamin A/C gene. Sex-determined expression of mutations in Dunnigan-type familial partial lipodystrophy and absence of coding mutations in congenital and acquired generalized lipoatrophy. Diabetes 49:1958–1962PubMedCrossRefGoogle Scholar
  69. Vigouroux C, Auclair M, Dubosclard E, Pouchelet M, Capeau J, Courvalin JC, Buendia B (2001) Nuclear envelope disorganization in fibroblasts from lipodystrophic patients with heterozygous R482Q/W mutations in the lamin A/C gene. J Cell Sci 114:4459–4468PubMedGoogle Scholar
  70. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein–ligand interactions. Protein Eng 8:127–134PubMedCrossRefGoogle Scholar
  71. Wolff N, Gilquin B, Courchay K, Callebaut I, Worman HJ, Zinn-Justin S (2001) Structural analysis of emerin, an inner nuclear membrane protein mutated in X-linked Emery–Dreifuss muscular dystrophy. FEBS Lett 501(2–3):171–176PubMedCrossRefGoogle Scholar
  72. Yokoyama C, Wang X, Briggs MR, Admon A, Wu J, Hua X, Goldstein JL, Brown MS (1993) SREBP-1, a basic-helix-loop-helix-leucine zipper protein that controls transcription of the low density lipoprotein receptor gene. Cell 75(1):187–197PubMedGoogle Scholar
  73. Young L, Jernigan RL, Covell DG (1994) A role for surface hydrophobicity in protein–protein recognition. Protein Sci 3(5):717–729PubMedCrossRefGoogle Scholar
  74. Zhang Z, Norris J, Schwartz C, Alexov E (2011) In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase. PLoS One 6(5):e20373PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Vidya Rajendran
    • 1
  • Rituraj Purohit
    • 1
  • Rao Sethumadhavan
    • 1
  1. 1.Bioinformatics Division, School of Bio Sciences and TechnologyVellore Institute of Technology UniversityVelloreIndia

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