Oshri Afanzar, Ph.D.

Biological switches · Quantitative biochemistry · Molecular organization

RESEARCH PORTFOLIO
BIOCHEMISTRY & BIOPHYSICS
From molecular interactions to collective behavior

How do biological systems switch states?

I study how molecular interactions give rise to biological switches—from the direction of a bacterial motor to the timing of cell division and the assembly of viral proteins on membranes.

My approach combines quantitative microscopy, biochemical reconstitution, and computational analysis to connect molecular mechanisms with biological behavior.

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Placeholder for an AFM image of NS5B assemblies on a supported lipid bilayer
NS5B forms broad, thin assemblies on membrane surfaces.
Research themes

Switches across biological scales

My work connects protein interactions, spatial organization, and nonlinear responses. Three systems have shaped this trajectory.

Membrane tethered NS5B recruits RNA to membrane surfaces
Membrane tethered NS5B recruits RNA to membrane surfaces.
Membranes & molecular assembly

The membrane as a regulatory environment

In reconstituted membrane systems, I examine how localization changes the assembly and RNA engagement of the hepatitis C virus polymerase NS5B. The work combines TIRF microscopy, FRAP, AFM, and solution biophysics.

Read the 2025 preprint »
Trigger waves of tubulin depolymerization and polymerization in Xenopus extract supplemented with sperm.
Afanzar et al., eLife (2020)
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Cell cycle & spatial dynamics

A nucleus that sets the pace

Using Xenopus egg extract, I investigated the origin of mitotic waves and showed that the nucleus serves as a pacemaker for the cell cycle. This work connects local biochemical regulation to coordinated behavior across space.

Read the eLife paper »
Automated analysis of bidirectional rotation of the bacterial flagellar motor.
Signaling & molecular mechanics

A switch with regulation and flexibility

My doctoral research examined how CheY signaling controls the bacterial rotary motor. Combining microscopy, statistical analysis, and modeling, I studied how tight regulation, flexibility, and ultrasensitivity can arise within one switching mechanism.

Find the EMBO Journal paper »
Proposed future research

Reconstructing complex biochemistry

I aim to study multicomponent protein systems in native-like environments, with a focus on the organization and function of viral transcription machinery.

  • Membrane-associated complexes: relate component stoichiometry and spatial organization to biochemical function.
  • Cell-free platforms: develop quantitative approaches to study complex biochemical reactions outside intact cells.
  • Sequence to function: connect protein variation with molecular mechanisms and reaction kinetics.
Research record

Publications

  1. 2025
  2. 2024
    CryoEM structures reveal how the bacterial flagellum rotates and switches direction

    Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM.

    Nature Microbiology 9, 1271–1281

  3. 2021
    The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility

    Afanzar O, Di Paolo D, Eisenstein M, Levi K, Plochowietz A, Kapanidis AN, Berry RM, Eisenbach M.

    The EMBO Journal 40, e104683

  4. 2020
    The nucleus serves as the pacemaker for the cell cycle

    Afanzar O, Buss GK, Stearns T, Ferrell JE Jr.

    eLife 9, e59989

  5. 2017
  6. 2016
    Single-molecule imaging of electroporated dye-labelled CheY in live Escherichia coli

    Di Paolo D, Afanzar O, Armitage JP, Berry RM.

    Philosophical Transactions of the Royal Society B 371, 20150492

  7. 2015
    CheY’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli

    Fraiberg M, Afanzar O, Cassidy CK, Gabashvili A, Schulten K, Levin Y, Eisenbach M.

    Molecular Microbiology 95, 231–244

  8. 2015
    Involvement of opsins in mammalian sperm thermotaxis

    Perez-Cerezales S, Boryshpolets S, Afanzar O, Brandis A, Nevo R, Kiss V, Eisenbach M.

    Scientific Reports 5, 16146

Scientific trajectory

About Oshri

My training spans biology, biochemistry, biophysics, and quantitative imaging. I began with genetics and enzymatic reactions, then turned to bacterial signaling, cell-cycle dynamics, protein allostery, and viral membrane systems.

I am interested in finding principles that explain how molecular interactions produce biological behavior. Developing experimental and computational tools has been central to that inquiry.

Stanford University · Priscilla Yang group
Membrane-associated viral polymerase assembly and RNA engagement
UC Berkeley · John Kuriyan group
CaMKII conformations, allostery, and kinetic reporters
Stanford University · James Ferrell group
Cell-cycle regulation and mitotic waves in Xenopus egg extract
Weizmann Institute of Science · Michael Eisenbach group
Doctoral research on bacterial flagellar motor switching
Teaching & scientific dialogue

Learning through inquiry

Mentoring and dialogue are integral to my scientific work. I have mentored technicians, undergraduate and master’s students, doctoral students, and postdoctoral researchers in experimental research, analysis, and scientific communication.

My teaching experience also includes tutoring high-school students in underserved communities and mentoring honors students through experimental projects.

Contact

For conversations about molecular switches, quantitative biochemistry, and research opportunities:

afanzar@gmail.com

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