The understanding at an atomic level of a broad range of cellular functions is a vital and strategic goal in biology. In many instances, these functions are performed by large macromolecular complexes, which have become known as """"""""molecular nano-machines."""""""" Naturally, these complexes show a large degree of molecular flexibility, or structural plasticity/heterogeneity, inherently associated with their tasks. This structural plasticity, in itself the key to the functional success of the molecular nano-machines, is a major cause of problems in the task of experimentally determining their three-dimensional (3D) structure. It has been postulated that three-dimensional electron microscopy (3D EM), and in particular its """"""""single-particle"""""""" and """"""""Tomography"""""""" variants, combined with the fitting of atomic-resolution structures, could be the right method to study these different conformational states. However, the image processing methodologies in the 3D EM field are not yet sufficiently developed so as to correctly overcome the difficulties that arise in the electron microscopic imaging, reconstruction and analysis of molecular nano-machines in the presence of structural flexibility. The need to develop a new set of image processing methodologies to address this issue is the central motivation for the proposed work. We will take a multi-disciplinary approach, which is based on a combination of understanding the techniques and applications of 3D EM with biological knowledge and mathematical and engineering expertise, to develop new technologies (in single particle 3D EM and in Tomography) to overcome outstanding problems of 3D EM imaging in the presence of structural heterogeneity. The proposed effort will concentrate on 3 interrelated lines of research in Image Preparation, Image Reconstruction, and Image Analysis, complemented by a rigorous approach to validating claims of superiority of any of the newly developed methods over those used in current practice. From the point of view of contribution to public health, we will be developing image processing methodologies for obtaining more accurate structural information by 3D EM (which is an essential instrumental tool of structural biology) than what can be achieved currently. This will contribute to our understanding of the detailed molecular mechanisms of some of the key cell functions and, consequently, impact on the field of drug discovery. The work is relevant in particular to cardiovascular and pulmonary disease and health and to blood research.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Project (R01)
Project #
5R01HL070472-06
Application #
7092575
Study Section
Special Emphasis Panel (ZRG1-MI (01))
Program Officer
Pandit, Sunil
Project Start
2001-09-01
Project End
2009-08-31
Budget Start
2006-09-01
Budget End
2007-08-31
Support Year
6
Fiscal Year
2006
Total Cost
$338,796
Indirect Cost
Name
CUNY Graduate School and University Center
Department
Biostatistics & Other Math Sci
Type
Other Domestic Higher Education
DUNS #
620128194
City
New York
State
NY
Country
United States
Zip Code
10016
Nikazad, T; Davidi, R; Herman, G T (2012) Accelerated perturbation-resilient block-iterative projection methods with application to image reconstruction. Inverse Probl 28:
Censor, Yair; Unkelbach, Jan (2012) From analytic inversion to contemporary IMRT optimization: radiation therapy planning revisited from a mathematical perspective. Phys Med 28:109-18
Stölken, Michael; Beck, Florian; Haller, Thomas et al. (2011) Maximum likelihood based classification of electron tomographic data. J Struct Biol 173:77-85
Melero, Roberto; Rajagopalan, Sridharan; Lázaro, Melisa et al. (2011) Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA. Proc Natl Acad Sci U S A 108:557-62
Censor, Y; Gibali, A; Reich, S (2011) The Subgradient Extragradient Method for Solving Variational Inequalities in Hilbert Space. J Optim Theory Appl 148:318-335
Garduño, E; Herman, G T; Davidi, R (2011) Reconstruction from a Few Projections by ?(1)-Minimization of the Haar Transform. Inverse Probl 27:
Sigworth, Fred J; Doerschuk, Peter C; Carazo, Jose-Maria et al. (2010) An introduction to maximum-likelihood methods in cryo-EM. Methods Enzymol 482:263-94
Kazantsev, Ivan G; Klukowska, Joanna; Herman, Gabor T et al. (2010) Fully three-dimensional defocus-gradient corrected backprojection in cryoelectron microscopy. Ultramicroscopy 110:1128-42
Lougovski, Pavel; LeNoach, Jordan; Zhu, Lei et al. (2010) Toward truly optimal IMRT dose distribution: inverse planning with voxel-specific penalty. Technol Cancer Res Treat 9:629-36
Scheres, Sjors H W (2010) Classification of structural heterogeneity by maximum-likelihood methods. Methods Enzymol 482:295-320

Showing the most recent 10 out of 56 publications