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Publications @ Colorado State University

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Splash image for Modular Scaffold Crystals paper

Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins

Ethan T. Shields, Caroline K. Slaughter, Fadwa Mekkaoui, Emma N. Magna, Cole Shepherd, Philip S. Lukeman, Donald E. Spratt, Christopher D. Snow.

  • BioRxiv Preprint

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    Illustration of the AI design of peptide-binding scFvs

    AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications

    Galindo G, Maejima D, DeRoo J, Burlingham SR, Fixen G, Morisaki T, Febvre HP, Hasbrook R, Zhao N, Ghosh S, Mayton EH, Snow CD, Geiss BJ, Ohkawa Y, Sato Y, Kimura H, Stasevich TJ, (2026) Science Advances.


    Diagram showing metal-organic frameworks deposited within porous protein crystal structure

    Deposition of Metal - Organic Frameworks within a Porous Protein Crystal Superstructure

    DeRoo JB, Rojina S, Jones AA, Rajendran D, Thai JE, Tuttle RR, Snow CD, Reynolds MM (2025) Journal of Materials Chemistry B.


    Laboratory automation setup showing liquid handling robotics for protein crystallization as well as Python programming control thereof

    Automation of Protein Crystallization Scaleup via Opentrons-2 Liquid Handling

    DeRoo JB, Jones AA, Slaughter CK, Ahr TW, Stroup SM, Thompson GB, Snow CD. (2025) SLAS Technology


    Scientific diagram showing DNA transport and adsorption in porous protein crystals

    Characterization of Guest DNA Transport and Adsorption within Host Porous Protein Crystals

    Chen S, Stuart JD, Munsky B, Snow CD. (2024) Langmuir.


    Image of crosslinked crystals withstanding tough conditions

    Tuning chemical DNA ligation within DNA crystals and protein-DNA co-crystals

    Orun AR, Slaughter CK, Shields ET, Vajapayajula A, Jones S, Shrestha R, Snow CD (2024) ACS Nanoscience Au.


    Image of a scFv bound to a peptide colored by AlphaFold confidence alongside a schematic illustration of a sliding window

    PAbFold: Linear Antibody Epitope Prediction using AlphaFold2

    DeRoo J, Terry JS, Zhao N, Stasevich TJ, Snow CD, Geiss BJ (2024) eLife.


    schematic illustrating catalytic, therapeutic, and structural biology applications of porous crystals

    Porous protein crystals: synthesis and applications

    Jones AA, Snow CD (2024) Chem. Commun.




    Laboratory Evolution of Substrate Recognition and Nanoparticle Product Size

    Hendricks A, Cohen R, McEwen G, Tien T, Guilliams B, Alspach A, Snow CD, Ackerson C (2024) ACS Chem. Biol.


    Image of PEG polymers inside protein crystal nanopores and probing thereof with an AFM tip

    Ligand presentation inside protein crystal nanopores: Tunable interfacial adhesion noncovalently modulates cell attachment

    Wang D, Hedayati M, Stuart JD, Madruga LYC, Popat KC, Snow CD, Kipper MP (2023) Materials Today Nano.


    Schematic image of a protein-dna co-crystal expanded with insert DNA with the insert acting as a binding site for a guest protein.

    Modular Protein-DNA Cocrystals as Precise, Programmable Assembly Scaffolds

    Orun, AR, Shields, ET, Dmytriw S, Vajapayajula A, Slaughter CK, and Snow CD (2023) ACS Nano.


    Image of fluorescent protein crystals conjugated to textiles.

    Textile Functionalization by Porous Protein Crystal Conjugation and Guest Molecule Loading

    Hartje LF, Andales DA, Gintner LP, Johnson LB, Li YV, Snow CD (2023) Crystals.


    schematic flowchart for the assembly of modular DNA synthetic barcodes.

    Scalable Combinatorial Assembly of Synthetic DNA for Tracking Applications

    Stuart JD, Wickenkamp NR, Davis KA, Meyer C, Kading RC, Snow CD (2023) Int. J. Mol. Sci.


    Schematic image of DNA barcodes being loaded into protein crystal nanopores and the crystals being fed to mosquito larvae, with adult mosquitoes flying away and being trapped.

    Mosquito Tagging Using DNA-Barcoded Nanoporous Protein Microcrystals

    Stuart JD, Hartman DA, Gray LI, Jones AA, Wickenkamp NR, Hirt C, Safira A, Regas AR, Kondash TM, Yates ML, Driga S, Snow CD, Kading RC (2022) PNAS Nexus


    Image of a DNA junction being ligated via the chemical EDC, and an illustration of crystals stable in low pH, blood serum, and deionized water.

    Stabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA

    Ward AR, Dmytriw S, Vajapayajula A, Snow CD, (2021) Crystals.


    AFM image showing the hexagonal array of nanopores in a protein crystal.

    Measuring interactions of DNA with nanoporous protein crystals by atomic force microscopy

    Wang D, Stuart JD, Jones AA, Snow CD, Kipper MJ (2021) Nanoscale.



    Design of genetically-encoded sensors to detect nucleosome ubiquitination in live cells

    Passos CDS, Choi Y-S, Snow CD, Cohen RE, Yao T. (2021) J Cell Biology


    Schematic image of scaffold building blocks and target macromolecules coming together to form a crystal

    Porous protein crystals as scaffolds for structural biology

    Ward AR, Snow CD (2020) Curr. Opin. Struct. Biol.


    Schematic image of a protein crystal nanopore array, with an inset closeup of a nanopore containing the enzymes HRP and GOx, working together to convert AmplexRed and Glucose into Resorufin.



    Porous protein crystals as scaffolds for enzyme immobilization

    Kowalski AE*, Johnson LB*, Dierl HK, Park S, Huber TR, Snow CD (2019) Biomater. Sci.


    Models of an enzyme active site

    Advancing biomarkers for anaerobic o-xylene biodegradation via metagenomic analysis of a methanogenic consortium

    Rossmassler K, Snow CD, Taggart D, Brown C, De Long SK (2019) Appl. Microbiol. Biotechnol.


    Diverse images of engineered protein crystals, both macroscopic and nanoscale features



    Protein crystal based materials for nanoscale applications in medicine and biotechnology

    Hartje LF, Snow CD (2018) WIREs Nanomedicine and Nanobiotechnology


    Image of a porous protein crystal, various cross-linking reagement chemical structures, a XRD pattern, and an image of healthy cells.



    Characterizing the Cytocompatibility of Various Cross-Linking Chemistries for the Production of Biostable Large-Pore Protein Crystal Materials

    Hartje LF, Bui HT, Andales DA, James SP, Huber TR, Snow CD. ACS Biomater. Sci. Eng. (2018)


    Schematic of a cysteine in a protein crystal nanopore getting conjugated to a guest molecule.



    Installing Guest Molecules at Specific Sites within Scaffold Protein Crystals

    Huber TR, McPherson EC, Keating CE, Snow CD. Bioconj. Chem. (2018) 29(1):17-22


    Image of a Au(25) gold nanoparticle with relative size to a protein crystal nanopore.



    Adsorbtion-Coupled Diffusion of Gold Nanoclusters Within a Large-Pore Protein Crystal Scaffold

    Hartje LF, Munsky B, Ni TW, Ackerson CJ, Snow CD. J Phys. Chem. B (2017) 121(32):7652-7659


    Image showing a protein crystal, the nanostructure thereof, and the effect of adding two different fluorescent proteins.

    Programmed Assembly of Host-Guest Protein Crystals

    Huber TR, Hartje LF, McPherson EC, Kowalski AE, Snow CD. Small (2016) 13(7):1602703


    Protein crystal schematic and showing the installation of gold nanoparticles via shared metal affinity.



    Gold Nanoparticle Capture Within Protein Crystal Scaffolds

    Kowalski AE, Huber TR, Ni TW, Hartje LF, Appel KL, Yost JW, Ackerson CJ, Snow CD. RSC Nanoscale (2016) 8(25):12693-6.


    Chart showing Rosetta energy scores for combinatorial libraries under consideration for protein design.

    A Structure-Based Design Protocol for Optimizing Combinatorial Protein Libraries

    Lunt MW, Snow CD. Methods Mol. Biol. (2016) 1414 99-138.


    Image showing a spatial grid, the action of fast-fourier transform, and a protein-crystal packing arrangement



    Optimizing Shape Complementarity Scoring Parameters for Recognition of Authentic Crystal Packing Arrangements

    Bennett JA, Snow CD. Cryst. Growth Des. (2016)


    Electrostatic surfaces for supercharged cellulase variants.



    Characterization of supercharged cellulase activity and stability in ionic liquids

    Johnson LB, Park S, Gintner LP, Snow CD. J. Mol. Catalysis. B: Enzymatic (2016) 132: 84-90


    Molecular structure for a cellulase



    Molecular dynamics simulations of cellulase homologs in aqueous 1-ethyl-3-methylimidazolium chloride

    Johnson LB, Snow CD. J. Biomol. Struct. Dyn. (2016)


    Image showing decomposition of cellulase into four blocks for recombination



    Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation

    Johnson LB, Gintner LP, Park S, Snow CD. P.E.D.S. (2015) 28(8): 259-267.


    Schematic of recombining protein blocks and subsequent experimental assaying and regression analysis

    Methods for Library-Scale Computational Protein Design

    Johnson LB, Huber TR, Snow CD. Methods Mol. Biol. (2014) 1216 129-59.


    Publications @ Caltech

    Close up view of selected sidechains in an enzyme active site



    Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes

    Mike Chen, Christopher Snow, Christina Vizcarra, Stephen Mayo, and Frances Arnold. Protein Eng. Des. Sel. (2012)
    View of a NADPH binding site in an enzyme



    Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methypropan-1-ol production at theoretical yield in Escherichia coli

    Sabine Bastian, Xiang Liu, Joseph Meyerowitz, Christopher Snow, Mike Chen, Frances Arnold. Metab. Eng. (2011), 13, 345-352.
    Close view of charged amino acid sidechains interacting with vectors to represent polarization effects.



    Polarizable Protein Packing

    Albert Ng and Christopher Snow J. Comp. Chem. (2011), 32, 1334-1344.
    Close-up view of amino acid sidechains in an enzyme active site



    Combinatorial alanine substitution enables rapid optimization of cytochrome P450BM3 for selective hydroxylation of large substrates

    Jared Lewis, Simone Mantovani, Yu Fu, Christopher Snow, Russell Komor, Chi-Huey Wong, and Frances Arnold. Chem. BioChem. (2010), 11, 2502-2505.
    Structure of a cellobiohydrolase enzyme



    Efficient screening of fungal cello-biohydrolase class I enzymes for thermo-stabilizing sequence blocks by SCHEMA structure-guided recombination

    Pete Heinzelman, Russell Komor, Arvind Kanaan, Philip Romero, Xinlin Yu, Shannon Mohler, Christopher Snow and Frances Arnold. Protein Engineering, Design and Selection (2010) dio: 10.1093/protein/gzq063
    Structure of a cellulase



    SCHEMA Recombination of a Fungal Cellulase Uncovers a Single Mutation that Contributes Markedly to Stability

    Pete Heinzelman, Christopher D. Snow, Matthew A. Smith, Xinlin Yu, Arbind Kannan, Kevin Boulware, Alan Villalobos, Sridhar Govindarajan, Jeremy Minshull, and Frances H. Arnold. J. Biol. Chem. (2009) 284:26229-26233.
    Structure of a cellulase with a substrate in the tunnel



    A Family of Thermostable Fungal Cellulases Created by Structure-Guided Recombination

    Pete Heinzelman, Christopher D. Snow, Indira Wu, Catherine Nguyen, Alan Villalobos, Sridhar Govindarajanm Jeremy Minshull and Frances H. Arnold. Proc. Natl. Acad. Sci. USA (2009) 106(14):5610-5615.
    Structure of a small protein showing many alternative rotamers



    SHARPEN: Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network

    Ilya V. Loksha, James R. Maiolo III, Cheng Hong, Albert Ng, and Christopher D. Snow. Journal of Computational Chemistry (2009) 30(6):999-1005.
    Structure of p450 enzyme active site



    Evolutionary history of the emergence of a specialized cytochrome P450 propane mono-oxygenase

    Rudi Fasan, Yergalem T. Meharenna, Christopher D. Snow, Thomas L. Poulos, and Frances H. Arnold. Journal of Molecular Biology (2008) 383(5), 1069-1080.
    Sphere representation of a mystery small molecule



    Hunting for predictive computational drug discovery models

    Christopher D. Snow. Expert Review of Anti-infective Therapy (2008) 6(3)
    Structure of a cytochrome P450



    A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments

    Yougen Li, Alan D. Drummond, Andrew M. Sawayama, Christopher D. Snow, Jesse D. Bloom, Frances H. Arnold. Nature Biotechnology (2007)


    Publications @ Stanford

    Structure of a ribosome



    Non-bulk-like Solvent Behavior in the Ribosome Exit Tunnel

    Del Lucent, Christopher Snow, Colin Aitken, Eric Sorin, Sung-Joo Lee & Vijay S. Pande. PLoS Comp. Bio. (2010), 6, e1000963.

    Side-chain recognition and gating in the ribosome exit tunnel

    Paula Petrone, Christopher D. Snow, Del Lucent & Vijay S. Pande. Proc. Natl. Acad. Sci. USA (2008) 105(43), 16549-16554.
    Structure of human aldose reductase enzyme



    Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory

    Ian Suydam, Christopher D. Snow, Vijay S. Pande & Stephen G. Boxer. Science (2006)
    Structure of N-terminal 39 residues of ribosomal protein L9



    Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates

    Christopher D. Snow, Young Min Rhee, & Vijay S. Pande. Biophysical Journal (2006)
    Structure of FKBP protein



    Direct calculation of the binding free energies of FKBP ligands

    Hideaki Fujitani, Yoshiaki Tanida, Masakatsu Ito, Guha Jayachandran, Christopher D. Snow, Michael R. Shirts, Eric J. Sorin, & Vijay S. Pande. Journal of Chemical Physics (2005) 123(8),084108

    How well can simulation predict kinetics and thermodynamics of protein folding?

    Christopher D. Snow, Eric Sorin, Young Min Rhee, & Vijay S. Pande. Annual Review of Biophysics and Biomolecular Structure
    Structure of p53 oligomerization domain



    Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations

    Lillian T. Chong, Christopher D. Snow, Young Min Rhee, & Vijay S. Pande. Journal of Molecular Biology (2004) 345(4), 869-78.
    Structure of Trp-zip miniprotein



    Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy

    Christopher D. Snow, Linlin Qiu, Deguo Du, Feng Gai, Stephen J. Hagen, & Vijay S. Pande. Proc. Natl. Acad. Sci. USA (2004) 101(12), 4077-4082.

    Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

    Nina Singhal, Christopher D. Snow, and Vijay S. Pande. The Journal of Chemical Physics (2004) 121(1) 415-425.
    Structure of the BBA5 miniprotein






    Absolute comparison of simulated and experimental protein-folding dynamics

    Christopher D. Snow, Houbi Nguyen, Vijay S. Pande, Martin Gruebele. Nature AOP, published online 20 October 2002; doi:10.1038/nature01160. Nature (2002) 420(6911), 102-106.


    Up Front: Science Behind the Screens

    HHMI Bulletin - M. Mitchell Waldrop
    Structure of Trp-Cage mini-protein

    The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations

    Christopher D. Snow, Bojan Zagrovic, Vijay S. Pande. J. Am. Chem. Soc. (2002) 124(49), 14548-14549.



    Native-like Mean Structure in the Unfolded Ensemble of Small Proteins

    Bojan Zagrovic, Christopher D. Snow, Siraj Khaliq, Michael R. Shirts, Vijay S. Pande. J. Mol. Biol. (2002) 323(1), 153-164.
    Structure of villin headpiece protein

    Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing

    Bojan Zagrovic, Christopher D. Snow, Michael R. Shirts, Vijay S. Pande. J. Mol. Biol. (2002) 323(5), 927-937.

    Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

    Vijay S. Pande, Ian Baker, Jarrod Chapman, Sidney Elmer, Stefan M. Larson, Young Min Rhee, Michael R. Shirts, Christopher D. Snow, Eric J. Sorin, Bojan Zagrovic. Biopolymers (2002) 68(1): 91-109.


    Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology

    Stefan M. Larson, Christopher D. Snow, Michael R. Shirts, Vijay S. Pande. Computational Genomics, Richard Grant, editor, Horizon Press

    Publications @ MIT

    Structure of ribosomal protein L9



    Surface Salt Bridges, Double-Mutant Cycles, and Protein Stability: an Experimental and Computational Analysis of the Interaction of the Asp 23 Side Chain with the N-Terminus of the N-Terminal Domain of the Ribosomal Protein L9

    Donna L. Luisi, Christopher D. Snow, Jo-Jin Lin, Zachary S. Hendsch, Bruce Tidor, Daniel P. Raleigh. Biochemistry (2003) 42(23), 7050-7060.





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