Keywords
Last Name

David Atkinson, PhD

TitleProfessor
InstitutionBoston University School of Medicine
DepartmentPhysiology & Biophysics
Address700 Albany St
Boston MA 02118
Phone(617) 638-4015
ORCID ORCID Icon0000-0002-4796-7396
Other Positions
TitleChairman of Physiology & Biophysics
InstitutionBoston University School of Medicine
DepartmentPhysiology & Biophysics

TitleResearch Professor
InstitutionBoston University School of Medicine
DepartmentBiochemistry

TitleGraduate Faculty (Primary Mentor of Grad Students)
InstitutionBoston University School of Medicine, Graduate Medical Sciences

 Awards and Honors

Start-EndDescription
2008Boston University Goldman School of Dental Medicine: Excellence in Teaching in the Basic Sciences
 Research Expertise & Professional Interests
The long standing objectives of my research are to provide the detailed structural and dynamic description of the plasma lipoproteins and apolipoproteins that is crucial to understanding the molecular mechanisms of such physiological processes as lipoprotein formation, receptor interactions, lipoprotein inter-conversions, and apoprotein exchange together with the changes in these characteristics that underlie the pathophysiology of atherosclerosis. Our research has been a component of a Program Project since its inception in 1980 and I have led the Program since 2001, taking over from Dr. Small. Building on initial training in diffraction methods and biophysics, I have maintained and expanded my expertise in state-of-the-art methods of molecular biophysics and structural biology including crystallography, electron microscopy/image processing, calorimetry and thermodynamics, circular dichroism, and molecular modeling/mechanics to probe the structure-function relationships of the lipoproteins and apolipoproteins. This includes a one year sabbatical at the MRC Laboratory of Molecular Biology, Cambridge, England developing electron microscopy.

My long standing research program has involved many collaborations with current and past Program Project investigators, particularly Drs. Gursky, Small, and McKnight. Our previous work over more than three decades has focused on the structural and thermodynamic properties of specific lipoproteins (HDL and LDL), and apolipoproteins, particularly apoA-1, together with studies of the LDL receptor. We derived the first structural description of HDL, nascent HDL and LDL using x-ray methods. Our mutation studies of the conformation, stability, and lipid binding properties have contributed to providing a framework for understanding the molecular properties of apoA-1. Furthermore, our studies of peptides representing segments of apoA-1, together with “idealized” sequence models, have provided information on the role of specific residues and domains, and their interactions in the structure and stability of apoA-1. For LDL, we pioneered the use of cryo-electron microscopy to study LDL structure and used mAb labeling to investigate the topology of apoB. In collaborations with Dr. Graham Shipley, a long standing collaborator and colleague, our approach for the LDL receptor has focused on structural studies of the functional extracellular domain of the receptor reconstituted into lipid vesicles.

 Self-Described Keywords
  • apolipoproteins
  • biophysical methods
  • lipoproteins
  • Molecular Biophysics
  • Structural Biology
  • structural electron microscopy
  • x-ray crystallography
 Publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
List All   |   Timeline
  1. Das M, Mei X, Jayaraman S, Atkinson D, Gursky O. Amyloidogenic mutations in human apolipoprotein A-I are not necessarily destabilizing - a common mechanism of apolipoprotein A-I misfolding in familial amyloidosis and atherosclerosis. FEBS J. 2014 Jun; 281(11):2525-42.
    View in: PubMed
  2. Wang L, Mei X, Atkinson D, Small DM. Surface behavior of apolipoprotein A-I and its deletion mutants at model lipoprotein interfaces. J Lipid Res. 2014 Mar; 55(3):478-92.
    View in: PubMed
  3. Gursky O, Jones MK, Mei X, Segrest JP, Atkinson D. Structural basis for distinct functions of the naturally occurring Cys mutants of human apolipoprotein A-I. J Lipid Res. 2013 Dec; 54(12):3244-57.
    View in: PubMed
  4. Khachfe HM, Atkinson D. Conformation and stability properties of B17: II. Analytical investigations using differential scanning calorimetry. Eur Biophys J. 2013 Apr; 42(4):309-14.
    View in: PubMed
  5. Khachfe HM, Atkinson D. Conformation and stability properties of B17: I. Analytical investigations using circular dichroism. Eur Biophys J. 2012 Aug; 41(8):639-46.
    View in: PubMed
  6. Gursky O, Mei X, Atkinson D. The crystal structure of the C-terminal truncated apolipoprotein A-I sheds new light on amyloid formation by the N-terminal fragment. Biochemistry. 2012 Jan 10; 51(1):10-8.
    View in: PubMed
  7. Mei X, Atkinson D. Crystal structure of C-terminal truncated apolipoprotein A-I reveals the assembly of high density lipoprotein (HDL) by dimerization. J Biol Chem. 2011 Nov 4; 286(44):38570-82.
    View in: PubMed
  8. Liu Y, Atkinson D. Immuno-electron cryo-microscopy imaging reveals a looped topology of apoB at the surface of human LDL. J Lipid Res. 2011 Jun; 52(6):1111-6.
    View in: PubMed
  9. Gorshkova IN, Atkinson D. Enhanced binding of apolipoprotein A-I variants associated with hypertriglyceridemia to triglyceride-rich particles. Biochemistry. 2011 Mar 29; 50(12):2040-7.
    View in: PubMed
  10. Xuan Gao, Shobini Jayaraman, Jeremiah Wally, Madhumita Guha, Mengxiao Lu, David Atkinson, Olga Gursky. Application of Circular Dichroism to Lipoproteins: Structure, Stability and Remodeling of Good and Bad Cholesterol. Circular Diichroism: Theory and Spectroscopy. Editor: David S. Rodgers. Nova Science Publishers, Inc. 2011.
  11. Liu Y, Luo D, Atkinson D. Human LDL core cholesterol ester packing: three-dimensional image reconstruction and SAXS simulation studies. J Lipid Res. 2011 Feb; 52(2):256-62.
    View in: PubMed
  12. Liu Y, Atkinson D. Enhancing the contrast of ApoB to locate the surface components in the 3D density map of human LDL. J Mol Biol. 2011 Jan 7; 405(1):274-83.
    View in: PubMed
  13. Gorshkova IN, Kypreos KE, Gantz DL, Zannis VI, Atkinson D. Biophysical properties of apolipoprotein E4 variants: implications in molecular mechanisms of correction of hypertriglyceridemia. Biochemistry. 2008 Nov 25; 47(47):12644-54.
    View in: PubMed
  14. Jiang ZG, Liu Y, Hussain MM, Atkinson D, McKnight CJ. Reconstituting initial events during the assembly of apolipoprotein B-containing lipoproteins in a cell-free system. J Mol Biol. 2008 Nov 28; 383(5):1181-94.
    View in: PubMed
  15. Wang L, Hua N, Atkinson D, Small DM. The N-terminal (1-44) and C-terminal (198-243) peptides of apolipoprotein A-I behave differently at the triolein/water interface. Biochemistry. 2007 Oct 30; 46(43):12140-51.
    View in: PubMed
  16. Zhu HL, Atkinson D. Conformation and lipid binding of a C-terminal (198-243) peptide of human apolipoprotein A-I. Biochemistry. 2007 Feb 13; 46(6):1624-34.
    View in: PubMed
  17. Gorshkova IN, Liu T, Kan HY, Chroni A, Zannis VI, Atkinson D. Structure and stability of apolipoprotein a-I in solution and in discoidal high-density lipoprotein probed by double charge ablation and deletion mutation. Biochemistry. 2006 Jan 31; 45(4):1242-54.
    View in: PubMed
  18. Wang L, Atkinson D, Small DM. The interfacial properties of ApoA-I and an amphipathic alpha-helix consensus peptide of exchangeable apolipoproteins at the triolein/water interface. J Biol Chem. 2005 Feb 11; 280(6):4154-65.
    View in: PubMed
  19. Zhu HL, Atkinson D. Conformation and lipid binding of the N-terminal (1-44) domain of human apolipoprotein A-I. Biochemistry. 2004 Oct 19; 43(41):13156-64.
    View in: PubMed
  20. Fang Y, Gursky O, Atkinson D. Lipid-binding studies of human apolipoprotein A-I and its terminally truncated mutants. Biochemistry. 2003 Nov 18; 42(45):13260-8.
    View in: PubMed
  21. Wang L, Atkinson D, Small DM. Interfacial properties of an amphipathic alpha-helix consensus peptide of exchangeable apolipoproteins at air/water and oil/water interfaces. J Biol Chem. 2003 Sep 26; 278(39):37480-91.
    View in: PubMed
  22. Fang Y, Gursky O, Atkinson D. Structural studies of N- and C-terminally truncated human apolipoprotein A-I. Biochemistry. 2003 Jun 10; 42(22):6881-90.
    View in: PubMed
  23. Gorshkova IN, Liu T, Zannis VI, Atkinson D. Lipid-free structure and stability of apolipoprotein A-I: probing the central region by mutation. Biochemistry. 2002 Aug 20; 41(33):10529-39.
    View in: PubMed
  24. Gorshkova IN, Liadaki K, Gursky O, Atkinson D, Zannis VI. Probing the lipid-free structure and stability of apolipoprotein A-I by mutation. Biochemistry. 2000 Dec 26; 39(51):15910-9.
    View in: PubMed
  25. Gursky O, Atkinson D. Thermodynamic analysis of human plasma apolipoprotein C-1: high-temperature unfolding and low-temperature oligomer dissociation. Biochemistry. 1998 Feb 3; 37(5):1283-91.
    View in: PubMed
  26. Gursky O, Atkinson D. High- and low-temperature unfolding of human high-density apolipoprotein A-2. Protein Sci. 1996 Sep; 5(9):1874-82.
    View in: PubMed
  27. Gursky O, Atkinson D. Thermal unfolding of human high-density apolipoprotein A-1: implications for a lipid-free molten globular state. Proc Natl Acad Sci U S A. 1996 Apr 2; 93(7):2991-5.
    View in: PubMed
  28. Spin JM, Atkinson D. Cryoelectron microscopy of low density lipoprotein in vitreous ice. Biophys J. 1995 May; 68(5):2115-23.
    View in: PubMed
  29. Nolte RT, Atkinson D. Conformational analysis of apolipoprotein A-I and E-3 based on primary sequence and circular dichroism. Biophys J. 1992 Nov; 63(5):1221-39.
    View in: PubMed
  30. D. Atkinson. Apolipoprotein structure: crystals and models. Current Opinion in Structural Biology, Current Biology, Ltd. 1992; 2:483-500.
  31. Kodali DR, Atkinson D, Small DM. Polymorphic behavior of 1,2-dipalmitoyl-3-lauroyl(PP12)- and 3-myristoyl(PP14)-sn-glycerols. J Lipid Res. 1990 Oct; 31(10):1853-64.
    View in: PubMed
  32. Walsh MT, Atkinson D. Calorimetric and spectroscopic investigation of the unfolding of human apolipoprotein B. J Lipid Res. 1990 Jun; 31(6):1051-62.
    View in: PubMed
  33. Reisinger RE, Atkinson D. Phospholipid/cholesteryl ester microemulsions containing unesterified cholesterol: model systems for low density lipoproteins. J Lipid Res. 1990 May; 31(5):849-58.
    View in: PubMed
  34. D.R. Kodali, D. Atkinson, D.M. Small. Molecular properties of glycerol derivatives. Proceedings 15th Scandinavian Symposium on Lipids, Rebild Bakker, Denmark, 11-15 June. 1989; 86-102.
  35. D.R. Kodali, D. Atkinson, D.M. Small. Molecular packing of 1,2-dipalmitoyl-3-decanoyl-_sn_-glycerol (PP10): Bilayer, Trilayer and hexalayer structures. J. Phys. Chem. 1989; 93(11):4683-4691.
  36. D.R. Kodali, D. Atkinson, D.M. Small. Influences of acyl chain length and unsaturation on the molecular packing of fats. Proceedings of the 1988 Nara Workshop on Functional Fats and Lipids, Oct. 4-6, Nara, Japan. The Society of Fats and Lipids Research and the Japan Oil Chemist's Society. 1988; 95-121.
  37. D.R. Kodali, D. Atkinson, D.M. Small . Influences of acyl chain length and unsaturation on the molecular packing of fats. J. Disp. Sci. Tech. 1988; 10:393-440.
  38. Walsh MT, Hamilton JA, Atkinson D, Small DM. Secondary and tertiary structure of apolipoproteins. Adv Exp Med Biol. 1988; 243:123-32.
    View in: PubMed
  39. Leduc R, Patton GM, Atkinson D, Robins SJ. Influence of different molecular species of phosphatidylcholine on cholesterol transport from lipoprotein recombinants in the rat. J Biol Chem. 1987 Jun 5; 262(16):7680-5.
    View in: PubMed
  40. Kodali DR, Atkinson D, Redgrave TG, Small DM. Structure and polymorphism of 18-carbon fatty acyl triacylglycerols: effect of unsaturation and substitution in the 2-position. J Lipid Res. 1987 Apr; 28(4):403-13.
    View in: PubMed
  41. Pittman RC, Glass CK, Atkinson D, Small DM. Synthetic high density lipoprotein particles. Application to studies of the apoprotein specificity for selective uptake of cholesterol esters. J Biol Chem. 1987 Feb 25; 262(6):2435-42.
    View in: PubMed
  42. Cladaras C, Hadzopoulou-Cladaras M, Nolte RT, Atkinson D, Zannis VI. The complete sequence and structural analysis of human apolipoprotein B-100: relationship between apoB-100 and apoB-48 forms. EMBO J. 1986 Dec 20; 5(13):3495-507.
    View in: PubMed
  43. Maulik PR, Atkinson D, Shipley GG. X-ray scattering of vesicles of N-acyl sphingomyelins. Determination of bilayer thickness. Biophys J. 1986 Dec; 50(6):1071-7.
    View in: PubMed
  44. Cistola DP, Atkinson D, Hamilton JA, Small DM. Phase behavior and bilayer properties of fatty acids: hydrated 1:1 acid-soaps. Biochemistry. 1986 May 20; 25(10):2804-12.
    View in: PubMed
  45. Walsh MT, Atkinson D. Physical properties of apoprotein B in mixed micelles with sodium deoxycholate and in a vesicle with dimyristoyl phosphatidylcholine. J Lipid Res. 1986 Mar; 27(3):316-25.
    View in: PubMed
  46. Atkinson D, Small DM. Recombinant lipoproteins: implications for structure and assembly of native lipoproteins. Annu Rev Biophys Biophys Chem. 1986; 15:403-56.
    View in: PubMed
  47. Walsh MT, Atkinson D. Reassembly of low-density lipoproteins. Methods Enzymol. 1986; 128:582-608.
    View in: PubMed
  48. Fahey DA, Small DM, Kodali DR, Atkinson D, Redgrave TG. Structure and polymorphism of 1,2-dioleoyl-3-acyl-sn-glycerols. Three- and six-layered structures. Biochemistry. 1985 Jul 2; 24(14):3757-64.
    View in: PubMed
  49. Kodali DR, Redgrave TG, Small DM, Atkinson D. Synthesis and polymorphism of 3-acyl-sn-glycerols. Biochemistry. 1985 Jan 15; 24(2):519-25.
    View in: PubMed
  50. Ginsburg GS, Walsh MT, Small DM, Atkinson D. Reassembled plasma low density lipoproteins. Phospholipid-cholesterol ester-apoprotein B complexes. J Biol Chem. 1984 May 25; 259(10):6667-73.
    View in: PubMed
  51. Atkinson D, Shipley GG. Structural studies of plasma lipoproteins. Basic Life Sci. 1984; 27:211-26.
    View in: PubMed
  52. D.R. Kodali, D. Atkinson, T.G. Redgrave, D.M. Small . Synthesis and polymorphism of 1,2-dipalmitoyl-3-acyl-sn-glycerols. JAOCS. 1984; 61(6):1078-1084.
  53. Ginsburg GS, Atkinson D, Small DM. Physical properties of cholesteryl esters. Prog Lipid Res. 1984; 23(3):135-67.
    View in: PubMed
  54. Walsh MT, Atkinson D. Solubilization of low-density lipoprotein with sodium deoxycholate and recombination of apoprotein B with dimyristoylphosphatidylcholine. Biochemistry. 1983 Jun 21; 22(13):3170-8.
    View in: PubMed
  55. Deckelbaum RJ, Halperin G, Atkinson D. Thermal transitions and structural properties of synthetic cholesterol alkyl and alkenyl ethers: analogues of biological cholesterol esters. J Lipid Res. 1983 May; 24(5):657-61.
    View in: PubMed
  56. D.M. Small, K. Miller, D. Cistola, G. Ginsburg, J. Parks, D. Atkinson, J.A. Hamilton. Physicochemical studies on the position of molecules in emulsions and membranes. Falk Symposium 33, in Bile Acids and Cholesterol in Health and Disease (eds. G. Paumgartner, A. Stiehl and W. Gerok). MTP Press, Ltd. 1983.
  57. Ginsburg GS, Small DM, Atkinson D. Microemulsions of phospholipids and cholesterol esters. Protein-free models of low density lipoprotein. J Biol Chem. 1982 Jul 25; 257(14):8216-27.
    View in: PubMed
  58. Clark SB, Atkinson D, Hamilton JA, Forte T, Russell B, Feldman EB, Small DM. Physical studies of d less than 1.006 g/ml lymph lipoproteins from rats fed palmitate-rich diets. J Lipid Res. 1982 Jan; 23(1):28-41.
    View in: PubMed
  59. Parks JS, Atkinson D, Small DM, Rudel LL. Physical characterization of lymph chylomicrons and very low density lipoproteins from nonhuman primates fed saturated dietary fat. J Biol Chem. 1981 Dec 25; 256(24):12992-9.
    View in: PubMed
  60. Ruocco MJ, Atkinson D, Small DM, Skarjune RP, Oldfield E, Shipley GG. X-ray diffraction and calorimetric study of anhydrous and hydrated N-palmitoylgalactosylsphingosine (cerebroside). Biochemistry. 1981 Oct 13; 20(21):5957-66.
    View in: PubMed
  61. Tall AR, Puppione DL, Kunitake ST, Atkinson D, Small DM, Waugh D. Organization of the core lipids of high density lipoproteins in the lactating bovine. J Biol Chem. 1981 Jan 10; 256(1):170-4.
    View in: PubMed
  62. Atkinson D, Small DM, Shipley GG. X-ray and neutron scattering studies of plasma lipoproteins. Ann N Y Acad Sci. 1980; 348:284-98.
    View in: PubMed
  63. A.L. Andrews, D. Atkinson, M.T.A. Evans, E.G. Finer, J.P. Green, M.C. Phillips, R.N. Robertson. The conformation and aggregation of bovine B-casein A. Part I. Molecular aspects of thermal aggregation. Biopolymers. 1979; 18:1105-1121.
  64. Tall AR, Small DM, Atkinson D, Rudel LL. Studies on the structure of low density lipoproteins isolated from Macaca fascicularis fed an atherogenic diet. J Clin Invest. 1978 Dec; 62(6):1354-63.
    View in: PubMed
  65. Atkinson D, Tall AR, Small DM, Mahley RW. Structural organization of the lipoprotein HDLc from atherosclerotic swine. Structural features relating the particle surface and core. Biochemistry. 1978 Sep 19; 17(19):3930-3.
    View in: PubMed
  66. D.M. Small, D. Atkinson, T. Redgrave, G.G. Shipley, A.R. Tall . A biophysical approach to cholesterol transport from tissues to bile. 4th International Symposium on Gallstones, Montreal, Canada. Hepatology-Research and Clinical Issues. Plenum Press. 1978; 4.
  67. Tall AR, Atkinson D, Small DM, Mahley RW. Characterization of the lipoproteins of atherosclerotic swine. J Biol Chem. 1977 Oct 25; 252(20):7288-93.
    View in: PubMed
  68. Atkinson D, Deckelbaum RJ, Small DM, Shipley GG. Structure of human plasma low-density lipoproteins: molecular organization of the central core. Proc Natl Acad Sci U S A. 1977 Mar; 74(3):1042-6.
    View in: PubMed
  69. Atkinson D, Smith HM, Dickson J, Austin JP. Interaction of apoprotein from porcine high-density lipoprotein with dimyristoyl lecithin. 1. The structure of the complexes. Eur J Biochem. 1976 May 1; 64(2):541-7.
    View in: PubMed
  70. Andrews AL, Atkinson D, Barratt MD, Finer EG, Hauser H, Henry R, Leslie RB, Owens NL, Phillips MC, Robertson RN. Interaction of apoprotein from porcine high-density lipoprotein with dimyristoly lecithin. 2. Nature of lipid-protein interaction. Eur J Biochem. 1976 May 1; 64(2):549-63.
    View in: PubMed
  71. G.G. Shipley, R.J. Deckelbaum, D. Atkinson, D.M. Small . Lipid organization in human plasma low density lipoproteins. Atherosclerosis IV, Proceedings of the IVth International Symposium on Atherosclerosis, Tokyo, Japan (eds. G. Schettler, Y.Goto, Y. Hata, G. Klose). Springer-Verlag. New York. 1976.
  72. Badley RA, Atkinson D, Hauser H, Oldani D, Green JP, Stubb JM. The structure, physical and chemical properties of the soy bean protein glycinin. Biochim Biophys Acta. 1975 Dec 15; 412(2):214-28.
    View in: PubMed
  73. D. Atkinson, Ph.D. Thesis. X-ray studies of the structure of natural and reassembled plasma high density lipoproteins. Council for National Academic Awards, England. 1975.
  74. Atkinson D, Davis MA, Leslie RB. The structure of a high density lipoprotein (HDL3) from porcine plasma. Proc R Soc Lond B Biol Sci. 1974 Jun 11; 186(083):165-80.
    View in: PubMed
  75. Atkinson D, Hauser H, Shipley GG, Stubbs JM. Structure and morphology of phosphatidylserine dispersions. Biochim Biophys Acta. 1974 Feb 26; 339(1):10-29.
    View in: PubMed
  76. Shipley GG, Atkinson D, Scanu AM. Small-angle x-ray scattering of human serum high-density lipoproteins. J Supramol Struct. 1972; 1(2):98-104.
    View in: PubMed
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