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2024

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Structural and functional insights into activation and regulation of the dynein-dynactin-NuMA complex

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Merve Aslan, Ennio A. d’Amico, Nathan H. Cho, Aryan Taheri, Yuanchang Zhao, Xinyue Zhong, Madeline Blaauw, Andrew P. Carter, Sophie Dumont, Ahmet Yildiz BioRxiv

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Stepping dynamics of dynein characterized by MINFLUX

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Joseph Slivka, Emma Gleave, Devinda P Wijewardena, John T Canty, Paul R Selvin, Andrew P Carter, Ahmet Yildiz BioRxiv

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NuMA mechanically reinforces the spindle independently of its partner dynein

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Nathan H Cho, Merve Aslan, Ahmet Yildiz, Sophie Dumont

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HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics

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Juan M. Perez-Bertoldi, Yuanchang Zhao, Akanksha Thawani, Ahmet Yildiz, Eva Nogales Nature Communications

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​Torques within and outside the human spindle balance twist at anaphase

 

Lila Neahring, Nathan H. Cho, Yifei He, Gaoxiang Liu, Jonathan Fernandes, Caleb J. Rux,  Konstantinos Nakos,  Radhika Subramanian,  Srigokul Upadhyayula, Ahmet Yildiz, Sophie Dumont JCB

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Protection of the Telomeric Junction by the Shelterin Complex

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Sajad Shiekh, Darion Feldt, Amanda Jack, Sineth G. Kodikara, Janan Alfehaid, Sabaha Pasha, Ahmet Yildiz, Hamza Balci JACS

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Nde1 is a Biphasic Regulator of the Dynein Activation Pathway

 

Yuanchang Zhao, Sena Oten, Ahmet Yildiz Nature Communications

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The mechanism and energetics of the dynein priming stroke

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Mert Golcuk, Sema Zeynep Yilmaz, Ahmet Yildiz, Mert Gur Structure

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Lis1 slows force-induced detachment of cytoplasmic dynein from microtubules

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Emre Kusakci, Zaw Min Htet, Yuanchang Zhao, John P. Gillies, Samara L. Reck-Peterson, Ahmet Yildiz Nature Chemical Biology

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A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression

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David Salvador-Garcia, Li Jin, Andrew Hensley, Mert Gölcük, Emmanuel Gallaud, Sami Chaaban, Fillip Port, Alessio Vagnoni, Vicente José Planelles-Herrero, Mark A McClintock, Emmanuel Derivery, Andrew P Carter, Régis Giet, Mert Gür, Ahmet Yildiz, Simon L Bullock JCB

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2023

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​​The Mechanism and Energetics of the Dynein Priming Stroke

 

Mert Golcuk, Sema Zeynep Yilmaz, Ahmet Yildiz, Mert Gur BioRxiv

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A force-sensitive mutation reveals a spindle assembly checkpoint-independent role for dynein in anaphase progression

 

David Salvador-Garcia, Li Jin, Andrew Hensley, Mert Gölcük, Emmanuel Gallaud, Sami Chaaban, Fillip Port, Alessio Vagnoni, Vicente José Planelles-Herrero, Mark A. McClintock, Emmanuel Derivery, Andrew P. Carter, Régis Giet, Mert Gür, Ahmet Yildiz, Simon L. Bullock BioRxiv

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TRAK adaptors coordinate the recruitment and activation of dynein and kinesin in mitochondrial transport

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John T. Canty*, Andrew Hensley*, Merve Aslan*, Amanda Jack, A Yildiz Nature Communications

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2022

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Compartmentalization of telomeres through DNA-scaffolded phase separation

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Amanda Jack, Yoonji Kim, Amy R Strom, Daniel SW Lee, Byron Williams, Jeffrey M Schaub, Elizabeth H Kellogg, Ilya J Finkelstein, Luke S Ferro, Ahmet Yildiz, Clifford P Brangwynne Developmental Cell

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Shelterin reduces the accessibility of telomeric overhangs

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Sajad Shiekh, Amanda Jack, Ayush Saurabh, Golam Mustafa, Sineth G Kodikara, Prabesh Gyawali, Mohammed Enamul Hoque, Steve Pressé, Ahmet Yildiz, Hamza Balci Nucleic Acids Research

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Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7

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Luke S. Ferro*, Qianglin Fang*, Lisa Eshun-Wilson*, Jonathan Fernandes*, Amanda Jack, Daniel P. Farrell, Mert Golcuk, Teun Huijben,  Katelyn Costa, Mert Gur, Frank DiMaio, Eva Nogales, Ahmet Yildiz Science

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SARS-Cov-2 Delta Variant Decreases Nanobody Binding and ACE2 Blocking Effectivity

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Mert Golcuk, Aysima Hacisuleyman, Sema Z Yilmaz, Elhan Taka, Ahmet Yildiz, Mert Gur J. Chem. Inf. Model.

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The Omicron variant increases the interactions of SARS-CoV-2 spike glycoprotein with ACE2

 

Mert Golcuk, Ahmet Yildiz, M Gur J Mol. Graphics and Model.

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2021

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Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptor

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Elhan Taka, Selma Z Yilmaz, Mert Golcuk, Ceren Kilinc, Umut Aktas, Ahmet Yildiz, Mert Gur The Journal of Physical Chemistry B

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Binding mechanism of neutralizing Nanobodies targeting SARS-CoV-2 Spike Glycoprotein

 

Mert Golcuk, Aysima Hacisuleyman, Burak Erman, Ahmet Yildiz, Mert Gur JCIM

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The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics

 

Andrea Serra-Marques, Ronja Houtekamer, Dorine Hintzen, John T Canty, Ahmet Yildiz, Sophie Dumont Journal of Cell Biology

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SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA

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Amanda Jack, Luke S. Ferro, Michael J. Trnka, Eddie Wehri, Amrut Nadgir, Xammy Nguyenla, Douglas Fox, Katelyn Costa, Sarah Stanley, Julia Schaletzky, Ahmet Yildiz. PLoS Biology

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2020

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Lis1 activates dynein motility by modulating its pairing with dynactin

 

Mohamed M Elshenawy, Emre Kusakci, Sara Volz, Janina Baumbach, Simon L Bullock & Ahmet Yildiz. Nature Cell Biology

 

Dynein harnesses active fluctuations of microtubules for faster movement

 

Yasin Ezber, Vladislav Belyy, Sinan Can & Ahmet Yildiz. Nature Physics

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2019

 

Cargo adaptors regulate stepping and force generation of mammalian dynein–dynactin

 

Mohamed M. Elshenawy *, John T. Canty *, Liya Oster, Luke S. Ferro, Zhou Zhou, Scott C. Blanchard & Ahmet Yildiz. Nature Chemical Biology  

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Kinesin-1 and dynein use distinct mechanisms to bypass obstacles

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Luke S. Ferro, Sinan Can, Meghan A. Turner, Mohamed M. Elshenawy, Ahmet Yildiz. eLife

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Rapid and Fully Microfluidic Ebola Virus Detection with CRISPR-CAS13A

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Peiwu Qin, Myeongkee Park, Kendra J. Alfson, Manasi Tamhankar, Ricardo Carrion, Jean L. Patterson, Anthony Griffiths, Qian He, Ahmet Yildiz, Richard Mathies, Ke Du. ACS Sensors

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Directionality of dynein is controlled by the angle and length of its stalk

 

Sinan Can *, Samuel Lacey *, Mert Gur, Andrew P. Carter and Ahmet Yildiz. Nature

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2018

 

MotAB-like machinery drives the movement of MreB filaments during bacterial gliding motility

 

Guo Fu, Jigar N. Bandaria, Anne Valérie Le Gall, Xue Fan, Ahmet Yildiz, Tâm Mignot, David R. Zusman and Beiyan Nan. PNAS

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Cryo-EM shows how dynactin recruits two dyneins for faster movement

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Linas Urnavicius*, Clinton K. Lau*, Mohamed M. Elshenawy, Edgar Morales-Rios, Carina Motz, Ahmet Yildiz & Andrew P. Carter.  Nature​

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2017

 

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.

 

Janice S. Chen, Yavuz S. Dagdas, Benjamin P. Kleinstiver, Moira M. Welch, Alexander A. Sousa, Lucas B. Harrington, Samuel H. Sternberg, J. Keith Joung, Ahmet Yildiz, Jennifer A. Doudna. Nature

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Dynamics of the IFT machinery at the ciliary tip

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Alexander Chien*, Sheng Min Shih*, Raqual Bower, Douglass Tritschler, Mary E Porter, Ahmet Yildiz.  eLife

 

A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9

 

Yavuz S. Dagdas*, Janice S. Chen*, Samuel H. Sternberg, Jennifer A. Doudna, Ahmet Yildiz.  Science Advances

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Covalent Protein Labeling and Improved Single-Molecule Optical Properties of Aqueous CdSe/CdS Quantum Dots

 

Sara M. Wichner, Victor R. Mann, Alexander S. Powers, Maya A. Segal, Mustafa Mir, Jigar N. Bandaria, Mark A. DeWitt, Xavier Darzacq, Ahmet Yildiz, Bruce E. Cohen.  ACS Nano

 

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9

 

Peiwu Qin*, Mahmut Parlak*, Cem Kuscu, Jigar Bandaria, Ritambhara Singh, Mustafa Mir, Xavier Darzacq, Ahmet Yildiz and Mazhar Adli. Nature Communications

 

PhotoGate microscopy to track single molecules in crowded environments

 

Vladislav Belyy, Sheng-Min Shih, Jigar Bandaria, Yongjian Huang, Rosalie E. Lawrence, Roberto Zoncu, Ahmet Yildiz. Nature Communications

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2016

 

The mammalian dynein-dynactin complex is a strong opponent to kinesin in a tug-of-war competition

 

Vladislav Belyy, Max A. Schlager, Helen Foster, Armando E. Reimer, Andrew P. Carter and Ahmet Yildiz. Nature Cell Biology

 

Shelterin Protects Chromosome Ends by Compacting Telomeric Chromatin

 

Jigar N. Bandaria, Peiwu Qin, Veysel Berk, Steven Chu and Ahmet Yildiz. Cell

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2015

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The polarity of myxobacterial gliding is regulated by direct interactions between the gliding motors and the Ras homolog MglA

 

Beiyan Nan, Jigar N. Bandaria, Kathy Y. Guo, Xue Fan, Ahmet Yildiz and David R. Zusman. PNAS

 

The AAA3 Domain of Cytoplasmic Dynein Acts as a “Switch” to Facilitate Microtubule Release

 

Mark A. Dewitt, Caroline A. Cypranowska, Vladislav Belyy and Ahmet Yildiz. NSMB

 

Single-molecule imaging of telomerase reverse transcriptase in human telomerase holoenzyme and minimal RNP complexes

 

Robert A. Wu, Yavuz S. Dagdas, S. Tunc Yilmaz, Ahmet Yildiz* and Kathleen Collins*. eLife

 

Kinesin's Front Head Is Gated by the Backward Orientation of Its Neck Linker

 

Yusra Satoglu-Dogan†, Sinan Can†, Frank B. Cleary, Vedud Purde and Ahmet Yildiz. Cell Reports

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2014

 

Cytoplasmic Dynein Transports Cargos via Load-Sharing between the Heads

 

Vladislav Belyy, Nathan L. Hendel, Alexander Chien and Ahmet Yildiz. Nature Communications

 

Tension on the linker gates the ATP-dependent release of dynein from microtubules

 

Frank B. Cleary, Mark A. Dewitt, Thomas Bilyard, Zaw Min Htet, Vladislav Belyy, Danna D. Chan, Amy Y. Chang and Ahmet Yildiz. Nature Communications

 

Bidirectional helical motility of cytoplasmic dynein around microtubules

 

Sinan Can, Mark A. Dewitt and Ahmet Yildiz. eLife

 

G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

 

Sujay Ray*, Jigar N. Bandaria*, Mohammad H. Qureshi, Ahmet Yildiz* and Hamza Balci*. PNAS

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  • “Single-Molecule Choreography between Telomere Proteins and G Quadruplexes”, Karl-Peter Hopfner. Structure

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2013

 

Intraflagellar transport drives flagellar surface motility

 

Sheng-Min Shih, Benjamin D Engel, Fatih Kocabas, Thomas Bilyard, Arne Gennerich, Wallace F Marshall, and Ahmet Yildiz. eLife

 

Flagella stator homologs function as motors for myxobacterial gliding motility by moving in helical trajectories

 

Beiyan Nan*, Jigar N. Bandaria*, Amirpasha Moghtaderi, Im-Hong Sun, Ahmet Yildiz* and David R. Zusman*. PNAS

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2012

 

Cytoplasmic Dynein Moves Through Uncoordinated Stepping of the AAA+ Ring Domains

 

Mark A. Dewitt, Amy Y. Chang, Peter A. Combs, and Ahmet Yildiz. Science

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  • “Molecular motors: A staggering giant”, Wilhelm J. Walter & Stefan Diez. Nature

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Pre-2012

 

Why kinesin is so processive

 

Erdal Toprak, Ahmet Yildiz, Melinda T. Hoffman, Steven S. Rosenfeld, and Paul R. Selvin. PNAS

 

Intramolecular strain governs kinesin stepping behavior along microtubules

 

Ahmet Yildiz, Michio Tomishige, Arne Gennerich, and Ron D. Vale.  Cell (Featured article)

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  • “Kinesin Motors: No Strain, No Gain”, Jared C. Cochran and F. Jon Kull. Cell

 

Single-Molecule Analysis of Dynein Processivity and Stepping Behavior.

 

Sam L. Reck-Peterson, Ahmet Yildiz†, Andrew P. Carter†, Arne Gennerich, Nan Zhang, and Ron D. Vale. Cell

 

Step-size is Determined by Neck Length in Myosin V

 

Takeshi Sakamoto, Ahmet Yildiz, Paul R. Selvin, and James R. Sellers. Biochemistry

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  • “Walk like a Molecular Motor”, Paul R. Selvin, The Scientist

 

Myosin VI walks hand-over-hand with its lever arm undergoing fluctuations when attached to actin

 

Ahmet Yildiz, Hyokeun Park, Dan Safer, Zhaohui Yang, Li-Qiong Chen, Paul R. Selvin, and H.Lee Sweeney. J. Bio. Chem

 

Kinesin walks hand-over-hand

 

Ahmet Yildiz, Michio Tomishige, Ron D. Vale, and Paul R. Selvin. Science

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Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5 nm localization

 

Ahmet Yildiz, Joseph N. Forkey, Sean A. McKinney, Taekjip Ha, Yale E. Goldman, and Paul R. Selvin. Science

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  • “Myosin Motors Walk the Walk”, C. Veigel & J. Molloy. Science

  • Breakthroughs of the year: The Runners-up, News and Editorial Staff. Science

  • Thomson ISR, one of the most cited papers in the research area of multidisciplinary (2003)

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*equal contribution

© Yildiz Lab  |  University of California, Berkeley

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