David Atkinson, Ph.D.

Professor and Chair, Department of Physiology & Biophysics

David Atkinson
  • Title Professor and Chair, Department of Physiology & Biophysics
  • Office W308C
  • Phone (617) 358-8448
  • Education B.Sc., (Hons) The City University, London, England
    Ph.D., The Council for National Academic Awards, England

Research Program

Plasma Lipoproteins and Apolipoproteins: Structure and Biology:

Cardiovascular disease, together with other diseases of lipid metabolism, remains the number one cause of health problems and death in Western society. The assembly and inter-conversions of the plasma lipoproteins, their receptor interactions, cofactor and enzyme substrate functions, and the cellular uptake of lipids and specific proteins play key roles in the overall regulation of lipid metabolism. Defects in lipid and lipoprotein metabolism express themselves at different levels of these processes. These defects lead to alterations in the composition, molecular structure and properties of the plasma lipoproteins, their apolipoproteins, and the receptors/transporters involved in lipid uptake or removal from cells. In turn, these changes contribute to the pathophysiology of diseases such as atherosclerosis. Ultimately, these physiological processes, together with associated pathophysiology, must be explained in terms of the molecular structures and the molecular interactions of the lipids, the apolipoproteins, and the enzymes and receptors/transporters with which they interact. However, these molecular details remain largely unknown. The long-term objectives of our research are to determine this molecular detail and to understand the structure-function relationships underlying these processes.

Fig. 1: Reverse Cholesterol Transport

High Density Lipoproteins (HDL) represent a heterogeneous population of nano-sized lipid-protein complexes (either discoidal or spherical particles) containing principally apoA-I that originates primarily from the liver.  The mechanisms of the well-documented anti-atherogenic role of HDL are related to its involvement in the pathways of reverse cholesterol transport (RCT).  In addition to providing the structural framework of HDL, apoA-I, the major protein of HDL, participates actively in the entire RCT pathway.  As illustrated in Figure 1, in the first and limiting step of RCT, apoA-I interacts with the ABCA1 transporter that plays a pivotal role to mediate the efflux of phospholipids and cholesterol from cells to form the nascent HDL particle.  Subsequently, apoA-I is a cofactor of the plasma enzyme LCAT that converts cholesterol into cholesterol ester resulting in the transformation of “nascent discoidal” HDL to mature “spherical” HDL.  Finally, apoA-I is the ligand for the SR-BI receptor that mediates selective cholesterol ester uptake from HDL by the liver.  However, it is now clear that it is not simply HDL levels that correlate with the anti-atherogenic function of HDL per se, but the ability of the HDL to efficiently promote cholesterol efflux and function in the pathway. These observations emphasize the need for molecular understanding of the mechanisms of HDL biogenesis. Our research focuses on further understanding of apoA-I, the structure of the ABCA1 transporter, and the molecular details of their interactions that drive the biogenesis of HDL.

Fig. 2: Δ(185-243)apoA-I Dimer Domain Swap. (PDB: 3R2P)

Apolipoprotein molecular features, particularly for apoA-I, have been derived from conformational analysis and our understanding has benefited from mutational approaches. The concept of the amphipathic -helix and the demonstration that the sequence of apoA-I is built from tandem repeats of 11 or 22 residues forming amphipathic helical segments has been central to this understanding. The interaction of apoA-I with phospholipids to form the discoidal “nascent” HDL particle has been studied extensively and it is now clear that apoA-I adopts a double belt organization at the periphery of the discoidal particle. Many of our previous studies contributed to this body of knowledge and led to our significant advance in solving the 2.2Å crystal structure of Δ(185-243)apoA-I (Figure 2). The molecular details revealed in the structure suggested new mechanistic hypotheses about the molecular features important in HDL biogenesis. The structure of Δ(185-243)apoA-I defined the molecular mechanism for the stabilization of apoA-I by the N-terminal, exon 3 encoded domain, and pointed to the role of dimerization in the assembly of HDL.

A movie showing the apoA-I structure

In addition, as also illustrated in Figure 2, the structure suggested how the central domain might function through domain swapping as a hinge region to facilitate the monomer to dimer conversion required for HDL formation. The structure also suggested that the central, flexible domain might form a tunnel to translocate lipids during the interaction with LCAT.

ATP-Binding Cassette Transporters (ABC) are a ubiquitous family of membrane proteins that exist across all organisms and function to transport a variety of substances into or out of cells driven by ATP hydrolysis. There are ~50 ABC transporters coded in the human genome that are divided into seven sub-families designated ABCA – ABCG (54). The 12-member ABCA sub-family, which includes ABCA1, is involved in moving lipid molecules across membranes (55). As illustrated in Figure 3, ABC transporters are composed of four core domains, two transmembrane domains with six helical segments, two highly conserved nucleotide-binding domains and two extracellular domains.

Fig. 3: Schematic Structure of ABCA1

In ABCA1, a single 2261-residue polypeptide chain forms the domains. ABCA transporters in general and ABCA1 in particular, contain two extracellular domains. These domains may be involved in interactions with other proteins such as apoA-I and may have regulatory functions. The general mechanism by which ABC transporters translocate substrate is through “alternating access”. Binding of ATP causes the two NBDs to tightly associate with two ATP molecules at the interface resulting in a conformation where the TMDs form an outward-facing cavity. ATP hydrolysis causes the NBDs to separate and drives conversion to an inward-facing cavity. The transport substrate selectivity is determined by the organization of the TMDs and the cavity formed by them. The mechanistic details of HDL biogenesis following apoA-I interaction with ABCA1 are not understood. The limited understanding of these mechanistic processes underscores the need for the detailed structural and molecular description that represents the central theme of our research. Thus building on our molecular understanding of apoA-I structure, our studies focus on structurally based mechanistic and functional investigations of apoA-I, the ABCA1 transporter, and their interactions.

Our primary approaches use the techniques of modern molecular biophysics and structural biology. These include protein crystallography, structural electron microscopy/image processing, calorimetry/thermodynamics, circular dichroism, and molecular modeling/mechanics to probe the structure and physical properties of lipoproteins, apolipoproteins, peptide models for the apolipoproteins, and lipid/apolipoprotein reassembled model systems.

A full list of publications is available at PubMed Central® (PMC) and here are our Journal Covers:


Research Group

Current Members
Xiaohu Mei, Ph.D., Instructor in Physiology & Biophysics
Irina Gorshkova, Ph.D., Senior Scientist
Angela Urdaneta, Graduate Student



Foundations of Biophysics and Structural Biology (GMS BY 763/3 – Graduate Medical Sciences):
This graduate level course provides a thorough grounding in the theory and major experimental methods of Biophysics and Structural Biology. The course covers protein thermodynamics, spectroscopy, electron microscopy, x-ray diffraction, crystallography, and NMR. The course provides both didactic and laboratory instruction.

Biophysics of Macromolecular Assemblies (GMS BY 776/7 – Graduate Medical Sciences)
This advanced course covers the concepts of the assembly of biomacromolecules, their structure and stabilizing forces, and biological function as related to structure. Examples are drawn from assemblies of proteins, lipids, lipoprotein systems, membranes and viruses.

Physiology of Specialized Cells (GMS FC707- Graduate Medical Sciences)
This course is one of the elective course modules (Module V) of the Foundations in Biomedical Sciences curriculum. Knowledge of cellular and molecular physiology is critical to understanding the higher order of functioning of tissues, organs, and organs systems. The objective of the course is to discuss the specialized adaptations of cells that help them to function in their respective tissues and organs.

Biochemistry (SDM MD 512 – School Dental Medicine)
This course is designed to acquaint the student with the basic principles of modern biochemistry. The topics to be covered include proteins, enzymes, DNA, RNA and protein synthesis, metabolism, lipids, connective tissue, and hormones and second messengers.

Human Medical Physiology A, B ( PH 730/731 – Graduate Medical Sciences):
The function of nerves, muscles, blood and the cardiovascular and digestive systems, function and regulation of the respiratory and renal systems, and endocrinology.

Physiology/Endocrinology/Neurophysiology (SDM MD 514 – School Dental Medicine)
This course presents the physiology of cells, tissues, organs, and integrated body functions, including the physiological basis for the understanding of clinical conditions. An integrated approach is taken to endocrinology and reproduction. Hormonal aberrations and their end-results in humans are presented in clinical correlations.

Principles Integrating Sciences and Medicine Curriculum (PrISM) (MS 141/2/4/5/6 –School of Medicine)
The first year integrated curriculum focused on the foundational sciences: Gross Anatomy, Histology, Human Behavior in Medicine, Biochemistry, Physiology, Genetics, Neuroscience, Endocrinology, and Immunology.

Contact Us

David Atkinson
Department of Physiology & Biophysics
Boston University School of Medicine
700 Albany Street, W308C
Boston MA 02118-2526

Phone:(617) 358-8448
e-mail: atkinson@bu.edu

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