Ahmet Yildiz

Ahmet Yildiz

Associate Professor

Office: 474 Stanley
Main: (510) 666-3792

Research Area(s): Biophysics

Biography

Ahmet Yildiz received his Ph.D. in Biophysics with Paul Selvin at University of Illinois Urbana-Champaign in 2004. After completing his postdoctoral work with Ron Vale at the University of California San Francisco, he joined the Physics Department at the University of California, Berkeley in 2008. 

 

Research Interests

Yildiz laboratory combines molecular biology and biophysical techniques to understand mechanisms that underlie the cellular organization and motility. Single molecule imaging enables direct observation of molecular motions, time courses of reactions and heterogeneity in subpopulations of the proteins. One major focus is to understand how microtubule motors work individually and how their interaction play a key role in intracellular transport and organismal motility. We are also using superresolution imaging techniques to visualize high order structures of telomeric DNA in human cells.

Current Projects

The projects in the lab combine techniques in physics, molecular biology and biochemistry to understand the mechanism of complex enzymatic machinery in vitro and in living cells. Major focus is on cytoplasmic dynein motor, intracellular cargo transport, and chromosome end protection.

Dissecting the Molecular Mechanism of Dynein: Cytoplasmic dynein is a AAA motor that transports a variety of intracellular cargo towards the microtubule minus-end in eukaryotic cells. Compared to other cytoskeletal motors (kinesin and myosin), the mechanism of dynein motility is significantly less understood due to its large size and complexity.  We showed that dynein motility differs significantly from kinesin and myosin in many aspects. By using single molecule high resolution tracking, FRET and optical trap microscopy, we are aiming to dissect the detailed mechanism of dynein processivity, directionality and force production. In addition, we introduce specific mutations in the motor domain and test the role of each subunit in dynein mechanism.

Single Molecule Studies on Intraflagellar Transport (IFT): We use Chlamydomonas model system to study the regulation of bidirectional cargo transport. Cilia and flagella power cell locomotion and mediate cell signaling in eukaryotes. Their assembly and maintenance require IFT between the flagellar membrane and axonemes. By using a combination of optical trap, multicolor fluorescence and FRAP microscopy, we showed that kinesin and dynein motors are coordinated in IFT such that only one type of motor remains active at a time. Chlamydomonas IFT is an excellent model system to study how motor protein activity is reciprocally coordinated to avoid tug-of-war in cargo transport. We aim to perform advanced microscopy assays in flagellar turnaround zones and reveal by which mechanism the cell turns the motors on and off. We also showed that IFT is responsible for gliding of the entire cell over a glass substrate. Gliding motility is central to understanding the function and evolution of cilia, as it might exist in early cilia before the establishment of axonemal beating. We aim to study how IFT dynamically turns over flagellar membrane proteins and facilitates mating between opposite gamete types. These studies will have broad implications for the traffic of signaling proteins within the ciliary membrane.

Maintenance and Protection of Mammalian Telomeres: Human telomeres consist of 2,000-30,000 base pairs of double-stranded TTAGGG repeats and terminate with a 50-200 nucleotide (nt) long single stranded 3’ G-overhang. The single-stranded telomeric DNA (ssTEL) is prone to enzymatic attack by exonucleases and DNA repair. We investigate how shelterin facilitates the protection of human telomeres both in vitro and in vivo. G-overhangs spontaneously fold into G-quadruplexes which also affect the competition between shelterin components and DNA repair proteins. We are also developing a single molecule assay to monitor telomerase activity in real time and study the interactions between shelterin, DNA structure and telomerase activity in model telomeric DNA. Telomere biology is central to human aging and cancer, and dissecting the mechanism of telomere protection and telomerase-based telomere elongation at a single molecule level will significantly advance the field.

Publications

Vladislav Belyy, Sheng-Min Shih, Jigar Bandaria, Yongjian Huang, Rosalie E. Lawrence, Roberto Zoncu, Ahmet Yildiz. PhotoGate Microscopy to Track Single Molecules in Crowded Environments.  Nature Communications 8:13978 (2017).

Vladislav Belyy, Max A. Schlager, Helen Foster, Armando E. Reimer, Andrew P. Carter and Ahmet Yildiz. The human dynein/dynactin complex is a strong opponent to kinesin in a tug-of-war competition. Nature Cell Biology 18(9):1018-24 (2016). 

Jigar N. Bandaria, Peiwu Qin, Veysel Berk, Steven Chu and Ahmet Yildiz. Shelterin Protects Chromosome Termini by Compacting Telomeric DNA. Cell 164(4):735-46 (2016).

Mark A. Dewitt, Caroline A. Cypranowska, Vladislav Belyy and Ahmet Yildiz. The AAA3 Domain of Cytoplasmic Dynein Acts as a “Switch” to Facilitate Microtubule Release. Nature Structural & Molecular Biology 22:73-80 (2015).

Sheng-Min Shih, Benjamin D Engel, Fatih Kocabas, Thomas Bilyard, Arne Gennerich, Wallace F Marshall and Ahmet Yildiz. Intraflagellar transport drives flagellar surface motility. eLife 2:e00744 (2013).

Mark A. Dewitt, Amy Y. Chang, Peter A. Combs, and Ahmet Yildiz. Cytoplasmic Dynein Moves Through Uncoordinated Stepping of the AAA+ Ring Domains. Science 335, 221-225 (2012).

Full list of publications can be found in my Google Scholar profile.