Craig W Vander Kooi, Ph.D.
Professor; Co-Director of Center for Spatial Biomolecule Research (CASBR); Assoc. Coordinator BMS/BMB PhD Program
Department:
MD-BIOCHEM / MOLECULAR BIOL
Business Phone:
(352) 294-8386
Business Email:
craig.vanderkooi@ufl.edu
About Craig W Vander Kooi
The Vander Kooi lab focuses on determining the mechanism of physical interactions underlying fundamental biological processes and human disease. The laboratory utilizes complimentary structural and mass-spectrometry based tools combined with biochemical, cellular, and animal model systems.
Through my training, I developed a profound appreciation for the power of atomic, molecular, and cellular spatial tools to provide deep biological insight. As a graduate student with Dr. Walter Chazin, I learned to use NMR and biochemical tools to describe the structure and interaction of proteins and developed a keen appreciation for the power of structural biology to provide deep biological insight on an atomic level. As a postdoctoral fellow with Dr. Daniel Leahy, I developed expertise in X-ray crystallography and biophysical tools to study receptor function, and developed a deep interest in understanding the basis for receptor cascades in key biological signaling pathways associated with disease.
Ongoing work includes: -Using the tools of structural biology to describe the mechanism of glucan kinases/phosphatases and engineer their function for therapeutic utilization, in collaboration with Dr. Matthew Gentry. -Understanding the molecular basis of hearing loss associated with mutations in GIPC3, in collaboration with Drs. Gregory Frolenkov and Bo Zhao. -Utilizing molecular spatial imaging as co-Director of the Center for Advanced Spatial Biomolecule Research (CASBR) at the University of Florida. Ongoing work with Drs. Ramon Sun and Matthew Gentry focuses on developing novel technologies to understand biological and pathological processes using MALDI-MSI.
Additional Positions:
Professor
2022 – Current
·
University of Florida College of Medicine
Professor
2020 – 2022
·
University of Kentucky
Associate Professor
2013 – 2020
·
University of Kentucky
Assistant Professor
2008 – 2013
·
University of Kentucky
Teaching Profile
Courses Taught
2023-2025
BCH6740 Physical Biochemistry/Structural Biology
2023-2024
BMS6031 Foundations of Med
2023-2024
DEN5121 Biochm Molec Cell Bio
Publications
Academic Articles
2025
AI-driven framework to map the brain metabolome in three dimensions.
Nature metabolism.
7(4):842-853
[DOI] 10.1038/s42255-025-01242-9.
[PMID] 40102678.
2025
CIB2 function is distinct from that of whirlin in the organization of sterocilia architecture.
Disease models & mechanisms.
18(3)
[DOI] 10.1242/dmm.052043.
[PMID] 40083274.
2025
Glycogen drives tumour initiation and progression in lung adenocarcinoma.
Nature metabolism.
[DOI] 10.1038/s42255-025-01243-8.
[PMID] 40069440.
2025
Protocol for high-power, brain-focused microwave fixation to define rodent metabolism.
STAR protocols.
6(2)
[DOI] 10.1016/j.xpro.2025.103794.
[PMID] 40287939.
2024
Alteration of Neuropilin-1 and Heparan Sulfate Interaction Impairs Murine B16 Tumor Growth.
ACS chemical biology.
19(8):1820-1835
[DOI] 10.1021/acschembio.4c00389.
[PMID] 39099090.
2024
CIB2 function is distinct from Whirlin in the development of cochlear stereocilia staircase pattern.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2024.07.30.605852.
[PMID] 39131343.
2024
Neurological glycogen storage diseases and emerging therapeutics.
Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics.
21(5)
[DOI] 10.1016/j.neurot.2024.e00446.
[PMID] 39277505.
2024
The crosstalk between neuropilin-1 and tumor necrosis factor-α in endothelial cells.
Frontiers in cell and developmental biology.
12
[DOI] 10.3389/fcell.2024.1210944.
[PMID] 38994453.
2024
The multifaceted roles of the brain glycogen.
Journal of neurochemistry.
168(5):728-743
[DOI] 10.1111/jnc.15926.
[PMID] 37554056.
2024
The Ruminococcus bromii amylosome protein Sas6 binds single and double helical α-glucan structures in starch.
Nature structural & molecular biology.
31(2):255-265
[DOI] 10.1038/s41594-023-01166-6.
[PMID] 38177679.
2023
Calcium and Integrin-binding protein 2 (CIB2) controls force sensitivity of the mechanotransducer channels in cochlear outer hair cells.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.07.09.545606.
[PMID] 37461484.
2023
MetaVision3D: Automated Framework for the Generation of Spatial Metabolome Atlas in 3D.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.11.27.568931.
[PMID] 38077043.
2023
Prognostic value of pathogenic variants in Lafora Disease: systematic review and meta-analysis of patient-level data.
Orphanet journal of rare diseases.
18(1)
[DOI] 10.1186/s13023-023-02880-6.
[PMID] 37658439.
2023
Spatial Metabolome Lipidome and Glycome from a Single brain Section.
bioRxiv : the preprint server for biology.
[DOI] 10.1101/2023.07.22.550155.
[PMID] 37546843.
2022
In situ mass spectrometry imaging reveals heterogeneous glycogen stores in human normal and cancerous tissues.
EMBO molecular medicine.
14(11)
[DOI] 10.15252/emmm.202216029.
[PMID] 36059248.
2022
The Toxoplasma glucan phosphatase TgLaforin utilizes a distinct functional mechanism that can be exploited by therapeutic inhibitors.
The Journal of biological chemistry.
298(7)
[DOI] 10.1016/j.jbc.2022.102089.
[PMID] 35640720.
2021
An empirical pipeline for personalized diagnosis of Lafora disease mutations.
iScience.
24(11)
[DOI] 10.1016/j.isci.2021.103276.
[PMID] 34755096.
2021
Brain glycogen serves as a critical glucosamine cache required for protein glycosylation.
Cell metabolism.
33(7):1404-1417.e9
[DOI] 10.1016/j.cmet.2021.05.003.
[PMID] 34043942.
2021
Cooperative Kinetics of the Glucan Phosphatase Starch Excess4.
Biochemistry.
60(31):2425-2435
[DOI] 10.1021/acs.biochem.1c00307.
[PMID] 34319705.
2021
Generation and characterization of a laforin nanobody inhibitor.
Clinical biochemistry.
93:80-89
[DOI] 10.1016/j.clinbiochem.2021.03.017.
[PMID] 33831386.
2021
Multimodal imaging and genetic findings in a case of ARSG-related atypical Usher syndrome.
Ophthalmic genetics.
42(3):338-343
[DOI] 10.1080/13816810.2021.1891552.
[PMID] 33629623.
2021
The 6th International Lafora Epilepsy Workshop: Advances in the search for a cure.
Epilepsy & behavior : E&B.
119
[DOI] 10.1016/j.yebeh.2021.107975.
[PMID] 33946009.
2020
Design, synthesis, and evaluation of a novel benzamidine-based inhibitor of VEGF-C binding to Neuropilin-2.
Bioorganic chemistry.
100
[DOI] 10.1016/j.bioorg.2020.103856.
[PMID] 32344185.
2020
Structural dissimilarity from self drives neoepitope escape from immune tolerance.
Nature chemical biology.
16(11):1269-1276
[DOI] 10.1038/s41589-020-0610-1.
[PMID] 32807968.
2019
Central Nervous System Delivery and Biodistribution Analysis of an Antibody-Enzyme Fusion for the Treatment of Lafora Disease.
Molecular pharmaceutics.
16(9):3791-3801
[DOI] 10.1021/acs.molpharmaceut.9b00396.
[PMID] 31329461.
2019
Immunization of Alpacas (Lama pacos) with Protein Antigens and Production of Antigen-specific Single Domain Antibodies.
Journal of visualized experiments : JoVE.
(143)
[DOI] 10.3791/58471.
[PMID] 30741259.
2019
Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.
Molecular therapy : the journal of the American Society of Gene Therapy.
27(2):300-313
[DOI] 10.1016/j.ymthe.2018.12.010.
[PMID] 30617019.
2019
Inhibition of Semaphorin3A Promotes Ocular Dominance Plasticity in the Adult Rat Visual Cortex.
Molecular neurobiology.
56(9):5987-5997
[DOI] 10.1007/s12035-019-1499-0.
[PMID] 30706367.
2019
N-glycosylation-defective splice variants of neuropilin-1 promote metastasis by activating endosomal signals.
Nature communications.
10(1)
[DOI] 10.1038/s41467-019-11580-4.
[PMID] 31420553.
2018
Oligomerization and carbohydrate binding of glucan phosphatases
Analytical Biochemistry.
563:51-55
[DOI] 10.1016/j.ab.2018.10.003.
[PMID] 30291838.
2018
T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability.
Nature chemical biology.
14(10):934-942
[DOI] 10.1038/s41589-018-0130-4.
[PMID] 30224695.
2017
How an alloreactive T-cell receptor achieves peptide and MHC specificity.
Proceedings of the National Academy of Sciences of the United States of America.
114(24):E4792-E4801
[DOI] 10.1073/pnas.1700459114.
[PMID] 28572406.
2017
Plate-Based Assay for Measuring Direct Semaphorin-Neuropilin Interactions.
Methods in molecular biology (Clifton, N.J.).
1493:73-87
[PMID] 27787843.
2016
An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry.
Structure (London, England : 1993).
24(7):1142-1154
[DOI] 10.1016/j.str.2016.04.011.
[PMID] 27238970.
2016
Angiotensinogen Exerts Effects Independent of Angiotensin II.
Arteriosclerosis, thrombosis, and vascular biology.
36(2):256-65
[DOI] 10.1161/ATVBAHA.115.306740.
[PMID] 26681751.
2016
Corrigendum: Structure and functions of angiotensinogen.
Hypertension research : official journal of the Japanese Society of Hypertension.
39(11)
[DOI] 10.1038/hr.2016.106.
[PMID] 27818490.
2016
Expanding the 3-O-Sulfate Proteome–Enhanced Binding of Neuropilin-1 to 3-O-Sulfated Heparan Sulfate Modulates Its Activity.
ACS chemical biology.
11(4):971-80
[DOI] 10.1021/acschembio.5b00897.
[PMID] 26731579.
2016
Novel role of 4-hydroxy-2-nonenal in AIFm2-mediated mitochondrial stress signaling.
Free radical biology & medicine.
91:68-80
[DOI] 10.1016/j.freeradbiomed.2015.12.002.
[PMID] 26689472.
2016
P-Rex1 Promotes Resistance to VEGF/VEGFR-Targeted Therapy in Prostate Cancer.
Cell reports.
14(9):2193-2208
[DOI] 10.1016/j.celrep.2016.02.016.
[PMID] 26923603.
2016
Structural biology of glucan phosphatases from humans to plants.
Current opinion in structural biology.
40:62-69
[DOI] 10.1016/j.sbi.2016.07.015.
[PMID] 27498086.
2016
Structural mechanisms of plant glucan phosphatases in starch metabolism.
The FEBS journal.
283(13):2427-47
[DOI] 10.1111/febs.13703.
[PMID] 26934589.
2016
The Tubulation Activity of a Fission Yeast F-BAR Protein Is Dispensable for Its Function in Cytokinesis.
Cell reports.
14(3):534-546
[DOI] 10.1016/j.celrep.2015.12.062.
[PMID] 26776521.
2015
Cys18-Cys137 disulfide bond in mouse angiotensinogen does not affect AngII-dependent functions in vivo.
Hypertension (Dallas, Tex. : 1979).
65(4):800-5
[DOI] 10.1161/HYPERTENSIONAHA.115.05166.
[PMID] 25691624.
2015
Mechanistic Insights into Glucan Phosphatase Activity against Polyglucan Substrates.
The Journal of biological chemistry.
290(38):23361-70
[DOI] 10.1074/jbc.M115.658203.
[PMID] 26231210.
2015
Neuropilin Functions as an Essential Cell Surface Receptor.
The Journal of biological chemistry.
290(49):29120-6
[DOI] 10.1074/jbc.R115.687327.
[PMID] 26451046.
2015
Oligomerization but Not Membrane Bending Underlies the Function of Certain F-BAR Proteins in Cell Motility and Cytokinesis.
Developmental cell.
35(6):725-36
[DOI] 10.1016/j.devcel.2015.11.023.
[PMID] 26702831.
2015
Structural basis for VEGF-C binding to neuropilin-2 and sequestration by a soluble splice form.
Structure (London, England : 1993).
23(4):677-87
[DOI] 10.1016/j.str.2015.01.018.
[PMID] 25752543.
2015
Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease.
Molecular cell.
57(2):261-72
[DOI] 10.1016/j.molcel.2014.11.020.
[PMID] 25544560.
2014
Computational design of the affinity and specificity of a therapeutic T cell receptor.
PLoS computational biology.
10(2)
[DOI] 10.1371/journal.pcbi.1003478.
[PMID] 24550723.
2014
Control of cellular motility by neuropilin-mediated physical interactions.
Biomolecular concepts.
5(2):157-66
[PMID] 25018786.
2014
Microplate-based screening for small molecule inhibitors of neuropilin-2/vascular endothelial growth factor-C interactions.
Analytical biochemistry.
453:4-6
[DOI] 10.1016/j.ab.2014.02.017.
[PMID] 24583243.
2014
Phosphoglucan-bound structure of starch phosphatase Starch Excess4 reveals the mechanism for C6 specificity.
Proceedings of the National Academy of Sciences of the United States of America.
111(20):7272-7
[DOI] 10.1073/pnas.1400757111.
[PMID] 24799671.
2014
Stoichiometry of the calcineurin regulatory domain-calmodulin complex.
Biochemistry.
53(36):5779-90
[DOI] 10.1021/bi5004734.
[PMID] 25144868.
2013
Effect of C-terminal sequence on competitive semaphorin binding to neuropilin-1.
Journal of molecular biology.
425(22):4405-14
[DOI] 10.1016/j.jmb.2013.07.017.
[PMID] 23871893.
2013
Fluorinated N,N-dialkylaminostilbenes repress colon cancer by targeting methionine S-adenosyltransferase 2A.
ACS chemical biology.
8(4):796-803
[DOI] 10.1021/cb3005353.
[PMID] 23363077.
2013
Functional Integration of the Conserved Domains of Shoc2 Scaffold.
PloS one.
8(6)
[DOI] 10.1371/journal.pone.0066067.
[PMID] 23805200.
2013
GLI1 regulates a novel neuropilin-2/α6β1 integrin based autocrine pathway that contributes to breast cancer initiation.
EMBO molecular medicine.
5(4):488-508
[DOI] 10.1002/emmm.201202078.
[PMID] 23436775.
2013
Mechanistic basis for the potent anti-angiogenic activity of semaphorin 3F.
Biochemistry.
52(43):7551-8
[DOI] 10.1021/bi401034q.
[PMID] 24079887.
2013
Megaprimer method for mutagenesis of DNA.
Methods in enzymology.
529:259-69
[DOI] 10.1016/B978-0-12-418687-3.00021-5.
[PMID] 24011052.
2013
SIN-dependent phosphoinhibition of formin multimerization controls fission yeast cytokinesis.
Genes & development.
27(19):2164-77
[DOI] 10.1101/gad.224154.113.
[PMID] 24115772.
2013
Structure of the Arabidopsis glucan phosphatase like sex four2 reveals a unique mechanism for starch dephosphorylation.
The Plant cell.
25(6):2302-14
[DOI] 10.1105/tpc.113.112706.
[PMID] 23832589.
2012
Function of members of the neuropilin family as essential pleiotropic cell surface receptors.
Biochemistry.
51(47):9437-46
[DOI] 10.1021/bi3012143.
[PMID] 23116416.
2012
Mechanism of selective VEGF-A binding by neuropilin-1 reveals a basis for specific ligand inhibition.
PloS one.
7(11)
[DOI] 10.1371/journal.pone.0049177.
[PMID] 23145112.
2012
Structural basis for selective vascular endothelial growth factor-A (VEGF-A) binding to neuropilin-1.
The Journal of biological chemistry.
287(14):11082-9
[DOI] 10.1074/jbc.M111.331140.
[PMID] 22318724.
2011
Systematic two-hybrid and comparative proteomic analyses reveal novel yeast pre-mRNA splicing factors connected to Prp19.
PloS one.
6(2)
[DOI] 10.1371/journal.pone.0016719.
[PMID] 21386897.
2010
A forward genetic screen in mice identifies Sema3A(K108N), which binds to neuropilin-1 but cannot signal.
The Journal of neuroscience : the official journal of the Society for Neuroscience.
30(16):5767-75
[DOI] 10.1523/JNEUROSCI.5061-09.2010.
[PMID] 20410128.
2010
Furin processing of semaphorin 3F determines its anti-angiogenic activity by regulating direct binding and competition for neuropilin.
Biochemistry.
49(19):4068-75
[DOI] 10.1021/bi100327r.
[PMID] 20387901.
2010
Structural basis for the glucan phosphatase activity of Starch Excess4.
Proceedings of the National Academy of Sciences of the United States of America.
107(35):15379-84
[DOI] 10.1073/pnas.1009386107.
[PMID] 20679247.
2010
The Prp19 WD40 domain contains a conserved protein interaction region essential for its function.
Structure (London, England : 1993).
18(5):584-93
[DOI] 10.1016/j.str.2010.02.015.
[PMID] 20462492.
2009
A link between aurora kinase and Clp1/Cdc14 regulation uncovered by the identification of a fission yeast borealin-like protein.
Molecular biology of the cell.
20(16):3646-59
[PMID] 19570910.
2008
Crystal structure of the CaV2 IQ domain in complex with Ca2+/calmodulin: high-resolution mechanistic implications for channel regulation by Ca2+.
Structure (London, England : 1993).
16(4):607-20
[DOI] 10.1016/j.str.2008.01.011.
[PMID] 18400181.
2007
Structural basis for ligand and heparin binding to neuropilin B domains.
Proceedings of the National Academy of Sciences of the United States of America.
104(15):6152-7
[PMID] 17405859.
2006
The Prp19 U-box crystal structure suggests a common dimeric architecture for a class of oligomeric E3 ubiquitin ligases.
Biochemistry.
45(1):121-30
[PMID] 16388587.
2005
Calcium-modulated S100 protein-phospholipid interactions. An NMR study of calbindin D9k and DPC.
Biochemistry.
44(17):6502-12
[PMID] 15850384.
2005
Structural and functional analysis of essential pre-mRNA splicing factor Prp19p.
Molecular and cellular biology.
25(1):451-60
[PMID] 15601865.
2005
The glucose-6-phosphatase catalytic subunit gene promoter contains both positive and negative glucocorticoid response elements.
Molecular endocrinology (Baltimore, Md.).
19(12):3001-22
[PMID] 16037130.
2003
Structural insights into the U-box, a domain associated with multi-ubiquitination.
Nature structural biology.
10(4):250-5
[PMID] 12627222.
2001
Mapping the interactions between flavodoxin and its physiological partners flavodoxin reductase and cobalamin-dependent methionine synthase.
Proceedings of the National Academy of Sciences of the United States of America.
98(17):9521-6
[PMID] 11493691.
2000
Magnetization transfer via residual dipolar couplings: application to proton-proton correlations in partially aligned proteins.
Journal of magnetic resonance (San Diego, Calif. : 1997).
143(2):435-9
[PMID] 10729274.
2000
Structural insights into substrate binding by the molecular chaperone DnaK.
Nature structural biology.
7(4):298-303
[PMID] 10742174.
1999
Line narrowing in spectra of proteins dissolved in a dilute liquid crystalline phase by band-selective adiabatic decoupling: application to 1HN-15N residual dipolar coupling measurements.
Journal of biomolecular NMR.
15(4):335-8
[PMID] 10685341.
Grants
Apr 2024
ACTIVE
Targeting Glycogen Metabolism in Ewing's Sarcoma: Diagnostic, Prognostic, and Therapeutic Applications
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Mar 2024
ACTIVE
Taperin-based macromolecular complex at the base of stereocilia
Role: Principal Investigator
Funding: INDIANA UNIV
via NATL INST OF HLTH NIDCD
Jan 2023
ACTIVE
Treatment of Lafora disease with antibody-enzyme fusion
Role: Co-Investigator
Funding: NATL INST OF HLTH NINDS
Nov 2022
ACTIVE
Aberrant Glycogen in Lung Adenocarcinoma Tumorigenesis
Role: Co-Investigator
Funding: NATL INST OF HLTH NCI
Oct 2022
– Sep 2023
MRI: Acquisition of Hydrogen/Deuterium eXchange Mass Spectrometer
Role: Other
Funding: NATL SCIENCE FOU
Sep 2022
ACTIVE
GIPC3, Multifunctional Myosin Adaptor in Mammalian Auditory Hair Cells
Role: Principal Investigator
Funding: UNIV OF KENTUCKY RESEARCH FOU
via NATL INST OF HLTH NIDCD
Contact Details
Phones:
- Business:
- (352) 294-8386
Emails:
- Business:
- craig.vanderkooi@ufl.edu
Addresses:
- Business Mailing:
-
PO Box 100245
Biochemistry & Molecular Biology
Gainesville FL 32610 - Business Street:
-
ARB R3-212
1200 Newell Drive
GAINESVILLE FL 32610