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Deniz Lab Single Molecule Biophysics Welcome to the Deniz Lab

Biophysics of Protein Complexity

Single Molecules to Mesoscale Cellular Compartments

Single-Molecule Biophysics. We develop and use single-molecule fluorescence methods to address key issues in molecular and cell biology. Single-molecule methods provide unprecedented views of structural and dynamic complexity in proteins and other biological macromolecules, allowing us to directly test biological models and theories (see review). A recent research focus is on Intrinsically Disordered Proteins (IDPs). While many proteins have well-defined 3-dimensional structures, IDPs have stretches of flexible sequence. IDPs are prevalent in proteomes, and their physics can play key roles in many cellular functions. Our single-molecule studies have shed light on the tunable nature of IDP structural landscapes (see paper), with implications for function (see paper) and diseases such as Parkinson’s and Alzheimer’s diseases (see paper 1, see paper 2). Recently, we have begun to probe mesoscale droplets formed by IDPs with RNA and other partners. These droplets are formed by liquid-liquid phase separation (see paper 1, paper 2), a process believed to be mechanistically key in the dynamics of membraneless cellular organelles such as the nucleolus.

Watch a video of how dynamic pattern and vacuole formation occur during non-equilibrium reentrent phase transitions in Protein-RNA droplets, relevent to cellular membraneless organelles.

YouTube link here    See paper in Angewandte Chemie

Watch a lecture (TSRI Faculty Lecture Series) about our work on single-molecule biophysics of protein disorder.

 YouTube link here

See blog post for National Institute of General Medical Sciences/NIH on Membrane-less Organelles that includes a discussion of our recent work; watch a related video.

Watch a lecture about our work on single-molecule and mesoscale biophysics of protein disorder at the NSF-Rice University Workshop: Modeling and Dynamics in Molecular Biophysics.

VIMEO link here

News and Outreach

  • Check out our new minireview article on the Physical Chemistry of Cellular Liquid Phase Separation – the accepted article is just out in Chemistry, a European Journal. Read about some of the key chemical and physical principles that underlie how cells compartmentalize biochemistry, surprising influences of active matter and dynamical effects, and emerging directions in the field. Congratulations to Emily and Ben!
  • Check out our new manuscript on bioRxiv, “Divalent cations can control a switch-like behavior in heterotypic and homotypic RNA coacervates”. The manuscript describes aspects of our work on mechanisms of functional cellular phase separation. Fluctuations in divalent ions are important in many cellular functions. Here, we show that divalent ions can strikingly switch protein-RNA systems between two types of phase separation regimes. The manuscript builds on previous work on these types of RNA phase separation (the first well known including from our work, and the second the subject of couple of recent papers), as well as on RNA folding. The resulting synthesis provides a unifying concept and simple mechanism for tuning the biochemical properties and function of membraneless organelles in response to changing cellular conditions. Congratulations to Paulo and Anthony!
  • Ashok to give lectures in 2018, at the University of Colorado, the IDP GRC (Switzerland), EMBO/EMBL Conference on cellular liquid separation and membraneless organelles, and Distinguished Faculty Lecture at the Skaggs Graduate School Annual Symposium, and in 2019, at the Laboratory of Chemical Physics/NIH, the UNAM Biotechnology Institute, the ACS National Meeting Symposium on "Getting to the bottom: optical and electron imaging of reactive chemical systems", and the Telluride Workshop on IDPs.
  • Two papers just out:
    • One in Cell Chemical Biology, our paper describes a convergent synthesis for generating labeled samples for 3-color single-molecule FRET protein studies. The method is expected to be especially useful for studies of dynamic complexity in intrinsically disordered proteins and in the context of membraneless cellular organelles. Congratulations to Crystal and Chris, and our collaborators Phil Cistrone and Phil Dawson!
    • Another in Biochemistry, our Perspective discusses recent discoveries and future directions on aspects of the polymer physics underlying dynamics and pattern formation in membraneless cellular organelles. These (droplet) compartments are important in cellular function and disease. Congratulations to Anthony!
  • Priya starts as an Assistant Professor in the Physics department at University at Buffalo (SUNY). Congratulations to Priya!
  • Jonathan Meng, previously a SURF summer intern in the lab, is named a 2017 Goldwater Scholar.
  • Ashok to give lectures in 2016 at the Protein Folding Dynamics GRC, Modeling & Dynamics workshop (VA), IDP GRS (faculty mentor), American Chemical Society meeting, University of Colorado, in 2017 at the Biophysical Society Meeting (Symposium), conference in Telluride, UC Berkeley Physical Chemistry, Computation/NMR GRC, and UC Berkeley Biophysics (Invitation by Graduate Students), and
  • Just out in Angewandte Chemie: Our work proposes and tests a new mechanism that addresses the physics of membraneless cellular organelles, which are dynamic cellular (droplet) compartments important in biology and disease. We show that a window-like behavior in RNA concentration controls both formation and dissolution of droplets. Strikingly, this reentrant transition can drive formation of substructures (vacuoles) with tunable lifetimes in the droplets. The paper was designated as a Very Important Paper in the journal, and was highlighted in the TSRI News and Views. Congratulations to Priya, Anthony, Mahdi and Paulo!
  • Chris and Mahdi defend their Ph.D. theses-congratulations!!!
  • Read News-Medical interview on some of our lab’s emerging research directions, including the effects of 2D-crowding on folding of a Parkinson’s disease-linked IDP.
  • Out in Angewandte Chemie: our paper reporting on the discovery that crowding in two dimensions (on a membrane) can force an intrinsically disordered protein (IDP) α-synuclein to adopt a hidden partially membrane-bound structure. The work reveals new layers of complexity and control of IDP structure, with implications for biological function. The paper was designated as a Hot Paper in the journal, highlighted in the Biophysical Society IDP subgroup Newsletter and the TSRI News and Views. Congratulations to Priya and Mahdi!
  • Congratulations! Ashok Deniz is named the 2016 TSRI Outstanding Mentor!"This was entirely a team effort - congratulations and many thanks to an amazing group of current and past graduate student and postdoctoral mentees!!"  Highlighted in TSRI News and Views.
  • Just out in ChemBioChem: our paper describing dual unnatural amino-acid incorporation for fluorescent dye labeling of the cancer related protein p97. Conventional labeling methods are a limitation for this large, multicysteine protein. The work permits single-molecule FRET studies of this cellular machine. Highlighted on the front cover of the journal issue. Congratulations to Chris, and collaborators Eli (UArizona), Pete, Minjin and ChanHyuk!
  • Out in Angewandte Chemie: our paper describing mechanistic studies of the disorder-order reaction of a multifunctional, cancer-related protein. We discovered alternative multi-step pathways for the reaction, that could be differentially tuned by biologically important phosphorylation and partner binding. Highlighted in Faculty of 1000 and TSRI News & Views. Congratulations to Priya, and St. Jude collaborators Richard and Diana!
  • See our paper in Nature Communications reporting development/application of a microfluidic temperature-jump method for studies of biochemical kinetics/dynamics. One application was to use oscillating temperature inputs to test the low-pass output behavior of a simple folding system. Highlighted in TSRI News & Views. Congratulations to Yann, Priya, and UCSD collaborators Alex Groisman, Mark and Mike!
  • Allan starts as an Assistant Professor at Baylor College of Medicine. Congratulations to Allan!
  • Ashok to give lectures in 2014 at Cornell University (Physics), Biophysical Society Thematic Meeting and IDP GRC (discussion leader), in 2015 at Washington University, St. Louis (Biochemistry), the American Physical Society meeting, the American Society for Biochemistry and Molecular Biology meeting, conferences in Telluride and Zurich, a keynote lecture at the Biophysical Society meeting IDP subgroup symposium.
  • Just out in Nature: our paper describing single-molecule studies that revealed strikingly complex patterns of modulation of allostery in a disordered protein, providing a novel biophysical mechanism for tunable cellular function. Congratulations to Allan and our collaborators Peter Wright and Josephine Ferreon. See the paper.  Highlighted in Nature News and Views, Chemical and Engineering News, Cell (Leading Edge Select), Faculty of 1000, and TSRI News and Views.
  • See our review article on protein folding studies at single-molecule resolution, published in Chemical Society Reviews.
  • Ashok to give a keynote lecture at the 2013 Chemical Biophysics Symposium (University of Toronto), invited lectures at the “Physics and Biology of Strongly Fluctuating Proteins” Symposium (University of Maryland) and the Scripps Research Faculty Lecture Series, and a Physical Chemistry Seminar (University of Wisconsin, Madison).
  • Our recent paper directly tests a hypothesis of counteraction between the effects of opposing chemical chaperones on the structural features of α-synuclein. The paper is slated to appear in a special issue of PNAS on the chemical physics of protein folding.
  • A recent paper sheds novel insight into the intricate mechanism of protein amyloid formation.
  • Undergraduate Asha continues her internship in the lab
  • Ashok to give invited talks in 2012 at Gordon Research Conferences (Protein Folding Dynamics; Intrinsically Disordered Proteins; Atomic and Molecular Interactions), St. Jude Children’s Research Hospital (Symposium on Biomolecular Structure, Dynamics and Function), Protein Society Meeting, and Pittcon
  • High-School teacher Lesli does a summer internship in the lab
  • Our recent Nature Methods Paper was highlighted in TSRI Press Release, Nature Methods News and Views, Physics Today Highlight, Faculty of 1000 Must Read Paper, ACS Chemical Biology Spotlight, PSI Nature Structural Biology Knowledgebase
  • Crystal presents to visiting high-school science teachers
  • Allan wins post-doctoral IDP subgroup award at the 2011 Biophysical Society Meeting
  • Allan, Crystal and Ashok speak at the 2011 Biophysical Society Meeting