International WorkshopProtein-DNA Interactions:
from Biophysics to Cancer Biology

December 5-6, 2019, Houston, Texas

PDI 2019 Abstract Book

2nd “Protein-DNA Interactions: from Biophysics to Cancer Biology” Workshop

Day 1: Thursday, December 5, 2019

Reception and Breakfast                                                                                         7:00 – 8:20am

Opening Remarks                             Anatoly Kolomeisky                                        8:20 – 8:30am

Session 1. Cancer-relevant protein-DNA interactions                            Chair: Guang Peng

1-1.      Ben E. Black (University of Pennsylvania)                                                     8:30 – 9:00am
Structural basis for allosteric PARP-1 DNA break retention and release

1-2.      Chin-Yo Lin (Univ. of Houston)                                                                     9:00 – 9:30am
Mapping and Modeling Estrogen Receptor Binding Sites: Basic Mechanisms and Relevance to Breast Cancer Biology

1-3.      Weixing Zhao (Univ. of Texas HSC San Antonio)                                         9:30 – 10:00am
Deciphering the DNA Binding Activities of BRCA1/2 in Genome Maintenance and Tumor Suppression

Session 2. Protein/DNA dynamics (I)                                             Chair: Junji Iwahara

2-1.      Peter Wolynes (Rice University)                                                                    10:20 – 10:50am
Protein-DNA Energy Landscapes from Transcription Factors to Chromosomes

2-2.      Ralf Metzler (University of Potsdam)                                                             10:50 – 11:20am
Geometry- and reaction-controlled diffusive search in gene regulation

2-3.      B. Montgometry Pettitt (Univ. of Texas Medical Branch)                               11:20 – 11:50am
DNA Confined

Poster graphical abstract presentations                                      
11:50 – 12:15pm

Lunch Break & Poster Session 1                                                                            12:15 – 1:30pm

Session 3. Chromatin biology, epigenetics, and cancer Chair: Courtney Hodges

3-1.      Alistair Boettiger (Stanford University)                                                           1:40 – 2:10pm
Highly multiplexed super-resolution imaging of chromatin structure

3-2.      Nicolas Young (Baylor College of Medicine)                                                 2:10 – 2:40pm
Single Molecule Combinations of Histone Post-translational Modifications Dynamically Regulate the Genome

3-3.      Wei Li (Baylor College of Medicine)                                                               2:40 – 3:10pm
Homeobox Oncogene Activation by Pan-Cancer DNA Hypermethylation


3-4.      Lacramioara Bintu (Stanford University)                                                        3:30 – 4:00pm
Controlling and measuring epigenetic regulation dynamics

3-5.      Stephen Mack (Baylor College of Medicine)                                                  4:00 – 4:30pm
Endogenous Retroviral Element Activation in Oncohistone Mutated Glioma

3-6.      Xiaodong Cheng (MD Anderson Cancer Center)                                          4:30 – 5:00pm
Detection of DNA modifications by sequence-specific transcription factors

Day 2: Friday, December 6, 2019

Breakfast                                                                                                                   7:30 – 8:20am
Session 4. Protein/DNA dynamics  (II)                                            Chair: Anatoly Kolomeisky
4-1.      José Nelson Onuchic (Rice University)                                                         8:30 – 9:00am
Protein sequence coevolution, energy landscapes and their connections to protein structure, folding and function

4-2.      Yuri Lyubchenko (University of Nebraska)                                                    9:00 – 9:30am
AFM to Directly Visualize Dynamics of protein-DNA complexes

4-3.      Margaret Cheung (University of Houston)                                                      9:30 – 10:00am
Proteins in a crowd under heat and pressure


4-4.      Marc C. Morais (Univ. of Texas Medical Branch)                                          10:20 – 10:50am
Mechanistic Implications of Symmetry Breaking in Viral dsDNA Packaging Motors

4-5.      Michael Diehl (Rice University)                                                                      10:50 – 11:20am
Demultiplexing the Multiple Overlapping Functions of Scaffold Proteins

4-6.      Oleg Igoshin (Rice University)                                                                       11:20 – 11:50am
Understanding Trade-offs in Biological Error Correction

Lunch & Poster Session 2                                                                                       11:50 – 1:00pm

Session 5. Transcription factors                                                    Chair: Chin-Yo Lin
5-1.      Charles Lin (Baylor College of Medicine)                                                      1:10 – 1:40pm
Targeting master transcription factor dependency in cancer

5-2.      Peter Vekilov (University of Houston)                                                             1:40 – 2:10pm
Unique Aggregation Behaviors of the Wild Type and Mutant Variants of the Transcription Factor p53


5-3.      Polly Fordyce (Stanford University)                                                               2:30 – 3:00pm
Leveraging Microfluidics for High-Throughput Studies of Transcription Factor/DNA Binding

5-4.      Elizabeth Komives (University of California San Diego)                                3:00 – 3:30pm
The functional fuzziness of the NFκB transcription activation domain

Poster awards                                                                                                           3:30 – 3:40pm

Keynote Presentation (Keck seminar) [web-broadcasted]                          Introduction: Chin-Yo Lin
Dr. Gordon Hager (National Cancer Institute)                                                4:00 – 5:00pm
New emergent properties of transcription factor dynamics in the mammalian nucleus

Closing Remarks                              Anatoly Kolomeisky                5:00 – 5:15pm