David Winogradoff

David Winogradoff
University of Illinois, Urbana-Champaign | UIUC · Department of Physics

Postdoc at Center for the Physics of Living Cells UIUC

About

20
Publications
2,955
Reads
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260
Citations
Citations since 2017
14 Research Items
245 Citations
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Introduction
Postdoc at the Center for the Physics of Living Cells in the Physics Department at the University of Illinois, Urbana-Champaign with Prof. Aleksei Aksimentiev, specializing in computational biophysics. Current research interests include modeling chromatin, detergent-induced protein unfolding, selective transport across the nuclear pore complex, viruses, and the crowded environment inside a living cell.
Additional affiliations
January 2016 - present
University of Illinois, Urbana-Champaign
Position
  • PostDoc Position
Description
  • My research focuses on computational models of chromatin, detergent-induced protein unfolding, selective transport across the nuclear pore complex, viruses, and the crowded environment inside a living cell.
January 2011 - December 2015
University of Maryland, College Park
Position
  • Research Assistant
Description
  • My research is highly interdisciplinary, spanning computer science, physics, chemistry, and biology. I earned a PhD in Chemical Physics investigating an individual nucleosome, the fundamental packaging unit of DNA in higher-order organisms.
June 2009 - June 2010
National Institute of Standards and Technology
Position
  • Guest Researcher
Description
  • My research was in fundamental physics, including a new method to detect neutrons and improving essential measurements for the Standard Model. I investigated Lyman Alpha Decay and Radiative Neutron Decay.
Education
September 2010 - August 2015
University of Maryland, College Park
Field of study
  • Chemical Physics
August 2005 - May 2009
Haverford College
Field of study
  • Mathematics

Publications

Publications (20)
Article
Full-text available
Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex’s pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of experimentally derived NPC structures with a theoretical model to determine the microsc...
Preprint
Full-text available
Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex's central pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of an experimentally-derived NPC structure with a theoretical model to determine t...
Article
Full-text available
The very chemical structure of DNA that enables biological heredity and evolution has non‐trivial implications for the self‐organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent...
Article
The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA–protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured...
Article
Full-text available
The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein--SDS comp...
Article
Full-text available
In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investiga...
Article
Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication, and repair, the DNA–histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA “breathe” by sponta...
Preprint
Full-text available
In eukaryotes, DNA is packaged through nucleosomes. Each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here we investigate the cano...
Article
Full-text available
Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during...
Article
Full-text available
The centromeric nucleosome is a key epigenetic determinant of centromere identity and function. Consequently, deciphering how CENP-A containing nucleosomes contribute structurally to centromere function is a fundamental question in chromosome biology. Here, we performed microsecond timescale all-atom molecular dynamics (MD) simulations of CENP-A an...
Article
Full-text available
Histone tails, the intrinsically disordered terminal regions of histone proteins, are key modulators of the structure and dynamics of chromatin, and consequently, are central to many template directed processes including DNA replication, repair and transcription. Acetylation of histone tails is a major post-translational modification (PTM) involved...
Article
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Thesis
Full-text available
The packaging of genomic information and the regulation of gene expression are both fundamentally important to eukaryotic life. Meters of human DNA must fit inside the micron-diameter nucleus while still rapidly becoming available for templated processes such as transcription, replication, and repair. Therefore, the DNA-protein complex known as chr...

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Projects

Project (1)
Project
Nucleosome and histones are the fundemental structural basis for chromatin. A good understanding of histone complex serves as the foundation for investigating the chromatin dynamics. In this project, we use computational modeling methods aiming to characterize the thermodynamics and kinetics of histone-related protein (and DNA) complex.