Biophotonics -- Top Collaborators

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Departments of Bioengineering, Molecular and Structural Biology, Pharmacology, Scripps Research Institute, Salk Institute for Biological Studies, Chemistry and Biochemistry, Biophotonics Technology Center

Gathered 07/17/2025 Editor: Frank Dininno

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Jin Zhang

Contact Information
profile	https://pharmacology.ucsd.edu/faculty/department-faculty/jin-zhang.html
email	jzhang32@health.ucsd.edu
department	Department of Pharmacology
title	Vice Chair, Professor
research focus	Genetically Encoded Fluorescent Biosensors
affiliations	Bio-Optical Probe Advancement Center
lab website	https://jinzhanglab.ucsd.edu/
publications	Google Scholar

Most-Cited Papers

1. 2002 Nature Creating new fluorescent probes for cell biology (2602)
2. 2001 PNAS Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering (751)
3. 2017 Cell The Growing and Glowing Toolbox of Fluorescent and Photoactive Proteins (722)
4. 2003 JCB A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C (675)

Most Recent Papers

1. 2025 Cell Aberrant phase separation of two PKA RIβ neurological disorder mutants leads to mechanistically distinct signaling deficits
2. 2025 Nature Far-red chemigenetic kinase biosensors enable multiplexed and super-resolved imaging of signaling networks
3. 2025 Nature Bright and photostable yellow fluorescent proteins for extended imaging
4. 2025 PNAS Lysosomal PIP3 revealed by genetically encoded lipid biosensors

Most Relevant Papers

1. 2019 Nature A genetically encoded near-infrared fluorescent calcium ion indicator
2. 2018 Nature Single-fluorophore biosensors for sensitive and multiplexed detection of signalling activities
3. 2015 Nature Ratiometric biosensors based on dimerization-dependent fluorescent protein exchange
4. 2007 RSC FRET-based biosensors for protein kinases: illuminating the kinome

Notes

Dr. Zhang’s lab does both fluorescence protein engineering and purification.

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Akif Tezcan

Contact Information

Contact Information
profile	https://matsci.ucsd.edu/faculty/akif-tezcan
email	tezcan@ucsd.edu
department	Department of Chemistry and Biochemistry
title	Professor
research focus	Protein Design\Analysis, Self-Assembled Crystal Arrays
affiliations	UCSD MRSEC
lab website	http://tezcan.ucsd.edu/
publications	Google Scholar

Most-Cited Papers

1. 2002 Science Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the FeMo-Cofactor (1362)
2. 2012 Nature Metal-directed, chemically tunable assembly of one-, two-and three-dimensional crystalline protein arrays (413)
3. 2005 RSA Structural basis of biological nitrogen fixation (410)
4. 1998 JACS Effects of ligation and folding on reduction potentials of heme proteins (327)

Most Recent Papers

1. 2025 JAC Efficient analysis of small-angle scattering curves for large biomolecular assemblies using Monte Carlo methods
2. 2025 ChemRxiv A de novo designed protein with versatile metal binding and tunable hydrolytic activity
3. 2025 JACS De Novo Design of Proteins for Autocatalytic Isopeptide Bond Formation
4. 2025 Cell Design of light-and chemically responsive protein assemblies through host-guest interactions

Relevant Papers

1. 2025 Cell Design of light-and chemically responsive protein assemblies through host-guest interactions
2. 2023 JACS Spatially patterned, porous protein crystals as multifunctional materials
3. 2022 Biochemistry Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices

Notes

Dr. Akif’s lab is capable of performing protein purification, as detailed in his lab website. However, his specialization is not in the field of fluorescence, but he does demonstrate the ability to tag his proteins by appending fluorescent proteins to them.

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Ashok Deniz

Contact Information
profile	https://www.scripps.edu/faculty/deniz/
email	deniz@scripps.edu
department	Department of Integrative Structural and Computational Biology
title	Professor
research focus	Single-Molecule Biopolymer Physics
affiliations	Scripps Research Institute
lab website	https://www.scripps.edu/deniz/
publications	Google Scholar

Most-Cited Papers

1. 1999 PNAS Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism (736)
2. 1999 PNAS Single-pair fluorescence resonance energy transfer on freely diffusing molecules: Observation of Förster distance dependence and subpopulations (703)
3. 2000 PNAS Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2 (586)
4. 2016 eLife Nucleophosmin integrates within the nucleolus via multi-modal interactions with proteins displaying R-rich linear motifs and rRNA (513)

Most Recent Papers

1. 2025 Cell BPS2025 - Exploring the structural diversity and condensate behavior of PopZ orthologs across α-proteobacteria
2. 2025 Cell BPS2025 - Biomolecular condensates induce local membrane potentials
3. 2025 Cell BPS2025 - Single-molecule conformational complexity in the disordered regions of fusion oncoproteins
4. 2025 Cell BPS2025 - Single-molecule FRET to study molecular mechanisms of biomolecular condensation

Most Relevant Papers

1. 2011 Nature Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing
2. 2008 ACS A General and Efficient Method for the Site-Specific Dual-Labeling of Proteins for Single Molecule Fluorescence Resonance Energy Transfer
3. 2002 ACS Unnatural Amino Acid Mutagenesis of Green Fluorescent Protein
4. 2001 ACS Monitoring the Conformational Fluctuations of DNA Hairpins Using Single-Pair Fluorescence Resonance Energy Transfer

Notes

Dr. Deniz seems to be more focused on imaging known proteins by attaching fluorophores to them rather than de novo protein engineering.

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David Millar

Contact Information
profile	https://www.scripps.edu/faculty/millar
email	millar@scripps.edu
department	Department of Integrative Structural and Computational Biology
title	Professor
research focus	Fluorescence Probing of Protein Conformational Dynamics
affiliations	Scripps Research Institute
lab website	https://www.scripps.edu/millar/Millar_Lab/Home.html
publications	Pubmed, Google Scholar

Most-Cited Papers

1. 1991 ACS Dynamics of mismatched base pairs in DNA (310)
2. 1999 Nature Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction (218)
3. 2002 ACS Solvent-Dependent Photoinduced Tautomerization of 2-(2‘-Hydroxyphenyl)benzoxazole (212)
4. 1982 AIP Torsion and bending of nucleic acids studied by subnanosecond time‐resolved fluorescence depolarization of intercalated dyes (192)

Most Recent Papers

1. 2025 eLife Distinct activation mechanisms of CXCR4 and ACKR3 revealed by single-molecule analysis of their conformational landscapes
2. 2025 Research Square Early HIV-1 Gag Assembly on Lipid Membrane with vRNA
3. 2023 frontiers Conformational Dynamics of DNA Polymerases Revealed at the Single-Molecule Level
4. 2023 Nucleic Acids Research Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics

Most Relevant Papers

1. 2021 eLIfe Single-molecule view of coordination in a multi-functional DNA polymerase
2. 2013 ACS Dynamics of site switching in DNA polymerase
3. 2011 JMB Single-molecule studies reveal that DEAD box protein DDX1 promotes oligomerization of HIV-1 Rev on the Rev response element
4. 2006 Angewandte Chemie Int. Ed. The Effects of Antibodies on Stilbene Excited-State Energetics