About

Zev Bryant is an Associate Professor of Bioengineering and, by courtesy, of Structural Biology at Stanford University. His laboratory focuses on understanding the physical mechanisms by which molecular motors convert chemical energy into mechanical work, which are essential to various biological processes such as DNA replication and vesicle transport. His research employs single molecule tracking and manipulation techniques to observe and perturb substeps in the mechanochemical cycles of individual motors, and utilizes protein engineering to explore the relationships between molecular structures and mechanical functions. His current research interests include torque generation by DNA-associated ATPases and mechanical adaptations of unconventional myosins. Bryant holds a B.Sc. in Biochemistry from the University of Washington (1998) and a Ph.D. in Molecular and Cell Biology from UC Berkeley (2003).

Research topics

• Computer Science
• Biophysics
• Biology
• Chemistry
• Biological system
• Physics
• Artificial Intelligence
• Genetics
• Materials science
• Engineering
• Chemical physics
• Optoelectronics
• Nanotechnology
• Biochemistry
• Library science
• Computational biology
• World Wide Web
• Statistical physics

Selected publications

• Stepwise DNA unwinding gates TnpB genome-editing activity

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-09 · 2 citations

  articleOpen access

  Abstract TnpB is a compact RNA-guided endonuclease and evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limited and its underlying determinants are poorly understood. Here, we used biochemical and single-molecule assays to examine the DNA-unwinding mechanism of Youngiibacter multivorans TnpB (Ymu1 TnpB). DNA unwinding proceeds through formation of a partially unwound intermediate state to a fully unwound open state. The open state forms inefficiently and collapses readily in the absence of negative supercoiling. An optimized variant, Ymu1-WFR, stabilizes formation of both the intermediate and open states, resulting in enhanced DNA cleavage in vitro and increased genome editing in vivo . These findings identify the physical basis for the observed minimal activities of natural TnpBs, revealing how stabilizing specific unwinding states enables efficient DNA targeting.

  PublisherDOI

• BPS2026 – Chiral motion in actomyosin systems: Exploring structural determinants through myosin protein engineering

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates

  Nature Communications · 2025-03-26 · 8 citations

  articleOpen accessSenior authorCorresponding

  The sequence specificity and programmability of DNA binding and cleavage have enabled widespread applications of CRISPR-Cas12a in genetic engineering. As an RNA-guided CRISPR endonuclease, Cas12a engages a 20-base pair (bp) DNA segment by forming a three-stranded R-loop structure in which the guide RNA hybridizes to the DNA target. Here we use single-molecule torque spectroscopy to investigate the dynamics and mechanics of R-loop formation of two widely used Cas12a orthologs at base-pair resolution. We directly observe kinetic intermediates corresponding to a ~5 bp initial RNA-DNA hybridization and a ~17 bp intermediate preceding R-loop completion, followed by transient DNA unwinding that extends beyond the 20 bp R-loop. The complex multistate landscape of R-loop formation is ortholog-dependent and shaped by target sequence, mismatches, and DNA supercoiling. A four-state kinetic model captures essential features of Cas12a R-loop dynamics and provides a biophysical framework for understanding Cas12a activity and specificity.

  PublisherOA PDFDOI

• BPS2025 - Ancestral RNA-guided TnpB nuclease interrogates DNA in discrete supercoiling-sensitive steps

  Biophysical Journal · 2025-02-01

  articleSenior author
  PublisherDOI

• BPS2025 - Ancestral RNA-guided TnpB nuclease interrogates DNA in discrete supercoiling-sensitive steps

  Biophysical Journal · 2025-02-01

  articleSenior author
  PublisherDOI

• Engineering filamentous myosins for optical control of contractility

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-23

  preprintOpen accessSenior authorCorresponding

  Abstract Understanding the behaviors of contractile actomyosin systems requires precise spatiotemporal control of filamentous myosin activity. Here, we develop a tool for optical control of contractility by extending the MyLOV family of gearshifting motors to create engineered filamentous myosins that change velocity in response to blue light. We characterize these minifilaments using in vitro single-molecule tracking assays, contractility assays in reconstituted actin networks, and imaging of contractile phenotypes in Drosophila S2 cells. The minifilaments change speed and/or direction when illuminated, display speeds that fall within and beyond the relevant physiological range, and display high processivities. Additionally, minifilament-driven contraction rates increase in blue light both in vitro and in S2 cells. Finally, we develop an alternative design for minifilaments that only interact processively with actin in blue light. Engineered minifilaments can be used to dissect behaviors such as self-organization and mechanotransduction in contractile systems both in vitro and in cells and tissues.

  PublisherOA PDFDOI

• BPS2025 - Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing

  Biophysical Journal · 2025-02-01 · 1 citations

  article
  PublisherDOI

• Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing

  Molecular Cell · 2025-04-23 · 18 citations

  articleOpen access

  RNA-guided CRISPR-Cas enzymes initiate programmable genome editing by recognizing a ∼20-base-pair DNA sequence next to a short protospacer-adjacent motif (PAM). To uncover the molecular determinants of high-efficiency editing, we conducted biochemical, biophysical, and cell-based assays on Streptococcus pyogenes Cas9 (SpyCas9) variants with wide-ranging genome-editing efficiencies that differ in PAM-binding specificity. Our results show that reduced PAM specificity causes persistent non-selective DNA binding and recurrent failures to engage the target sequence through stable guide RNA hybridization, leading to reduced genome-editing efficiency in cells. These findings reveal a fundamental trade-off between broad PAM recognition and genome-editing effectiveness. We propose that high-efficiency RNA-guided genome editing relies on an optimized two-step target capture process, where selective but low-affinity PAM binding precedes rapid DNA unwinding. This model provides a foundation for engineering more effective CRISPR-Cas and related RNA-guided genome editors.

  PublisherDOI

• Rapid two-step target capture ensures efficient CRISPR-Cas9-guided genome editing

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-10-02 · 5 citations

  preprintOpen accessCorresponding

  SUMMARY RNA-guided CRISPR-Cas enzymes initiate programmable genome editing by recognizing a 20-base-pair DNA sequence adjacent to a short protospacer-adjacent motif (PAM). To uncover the molecular determinants of high-efficiency editing, we conducted biochemical, biophysical and cell-based assays on S. pyogenes Cas9 ( Spy Cas9) variants with wide-ranging genome editing efficiencies that differ in PAM binding specificity. Our results show that reduced PAM specificity causes persistent non-selective DNA binding and recurrent failures to engage the target sequence through stable guide RNA hybridization, leading to reduced genome editing efficiency in cells. These findings reveal a fundamental trade-off between broad PAM recognition and genome editing effectiveness. We propose that high-efficiency RNA-guided genome editing relies on an optimized two-step target capture process, where selective but low-affinity PAM binding precedes rapid DNA unwinding. This model provides a foundation for engineering more effective CRISPR-Cas and related RNA-guided genome editors.

  PublisherOA PDFDOI

• Motor crosslinking augments elasticity in active nematics

  Soft Matter · 2024-01-01 · 12 citations

  articleOpen access

  In active materials, uncoordinated internal stresses lead to emergent long-range flows. An understanding of how the behavior of active materials depends on mesoscopic (hydrodynamic) parameters is developing, but there remains a gap in knowledge concerning how hydrodynamic parameters depend on the properties of microscopic elements. In this work, we combine experiments and multiscale modeling to relate the structure and dynamics of active nematics composed of biopolymer filaments and molecular motors to their microscopic properties, in particular motor processivity, speed, and valency. We show that crosslinking of filaments by both motors and passive crosslinkers not only augments the contributions to nematic elasticity from excluded volume effects but dominates them. By altering motor kinetics we show that a competition between motor speed and crosslinking results in a nonmonotonic dependence of nematic flow on motor speed. By modulating passive filament crosslinking we show that energy transfer into nematic flow is in large part dictated by crosslinking. Thus motor proteins both generate activity and contribute to nematic elasticity. Our results provide new insights for rationally engineering active materials.

  PublisherOA PDFDOI

Recent grants

• Structural Dynamics and Mechanochemical Coupling in Nucleoprotein Machines

  NIH · $2.7M · 2014–2026

• NIH Grant DP2OD004690

  NIH · $2.4M · 2013

• Engineering Cytoskeletal Motors

  NIH · $1.3M · 2018–2023

Frequent coauthors

• Carlos Bustamante

  University of California, Berkeley

  49 shared

• Michael D. Stone

  Cardiff and Vale University Health Board

  45 shared

• Jeff Gore

  Massachusetts Institute of Technology

  36 shared

• Seok‐Cheol Hong

  Korea University

  30 shared

• Paul V. Ruijgrok

  Stanford University

  24 shared

• Nicholas R. Cozzarelli

  20 shared

• Nancy J. Crisona

  15 shared

• Steven B. Smith

  15 shared