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Publications

PNAS Spider Silk Paper Published

We’re excited to share our latest paper, now published in PNAS — and a strong way to close out the year with paper #10 from the lab. https://www.pnas.org/doi/10.1073/pnas.2523198122 In this study, we address a long-standing question in spider silk biology: how do soluble, intrinsically disordered silk proteins transition through liquid–liquid phase separation (LLPS) into highly ordered, β-sheet-rich fibers?By combining residue-specific solution NMR, DNP-enhanced solid-state NMR, molecular dynamics simulations, and AlphaFold3 modeling, we show that arginine–tyrosine cation–π interactions act as key molecular “stickers” that both drive phase separation and persist into the final fiber architecture. Phosphate triggers LLPS without inducing premature β-sheet formation, instead reorganizing side-chain interactions that later nucleate structural order.Importantly, we directly observe Arg–Tyr contacts in native spider silk fibers and demonstrate that arginine is partially incorporated at β-sheet interfaces, while tyrosine frequently adopts interfacial or β-turn-like conformations. This provides a mechanistic link between sequence-encoded chemistry, condensate formation, and hierarchical materials assembly in a natural structural protein.Beyond spider silk, these findings offer a general framework for understanding how weak, multivalent interactions bridge disordered and ordered states in phase-separating protein systems — with implications for biomaterials design and other biological condensates.This work was funded by the U.S. Department of Defense – Air Force Office of Scientific Research (AFOSR).Huge congratulations to the team, especially the co-first authors, Hannah Johnson and Kevin Chalek and sincere thanks to our collaborators Chris Lorenz (KCL) and Galia Debelouchina (UCSD) for making this work possible. ...

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New Spider Silk Publication in PNAS Nexus

Thrilled to share that our PNAS Nexus paper is now online as an Advance Article , the culmination of more than five years of work. "Sequence-Encoded Tubular Architectures in Disordered Spider Silk Proteins Revealed by Multiscale Simulations and NMR" https://academic.oup.com/pnasnexus/article/4/12/pgaf378/8363280?login=true This project started with a simple question that has puzzled the spider silk field for decades: How can these massive, intrinsically disordered spidroin proteins stay soluble at extremely high concentration yet, be instantly ready to assemble into one of the toughest materials known? Answering it required: 🔹 Multiscale MD simulations (coarse-grained MARTINI 2 & 3 + atomistic CHARMM36m/IDPSFF)🔹 SAXS ensemble modeling over 2,581 conformers🔹 Solution NMR backbone assignments of notoriously difficult IDP-like sequences🔹 Custom tools developed by Chris Imboden-Forman (Vesiform, pdbProc, pdbStapler)🔹 And a lot of persistence. What we found is both surprising and satisfying: Spider silk proteins form dynamic ensembles that include metastable tubular architectures ~3–4 nm in diameter and ~50 nm long — a minority population, but absolutely required to reconcile SAXS and NMR data. These tubules arise from sequence-encoded amphiphilic patterning: hydrophobic poly(Ala) packs the core, while polar Tyr/Gln/Arg residues in Gly-Gly-X motifs stabilize the surface. SAXS shows you can’t fit the data without them. NMR and atomistic MD reveal they remain highly dynamic and IDP-like while exhibiting a high beta-turn content that explain the compactness. It took: 💻 Multiple years of aggregate GPU time,🧪 Hundreds of NMR hours,🔍 Countless ensemble fits, simulations, and mutational studies —but seeing this model come together has been incredibly rewarding.Huge congratulations to Chris Imboden-Forman Forman (who drove the computational/modeling effort), David Onofrei (NMR), Dillan Stengel, Julian Aldana, Christopher Paolini, and my collaborator Nathan Gianneschi. This was truly a team achievement. Grateful to DOD-AFOSR for supporting this effort and to everyone who contributed along the way. ...

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Silk Mass Photometry Paper Published in JPCL

"Distinct Dimerization Mechanisms in Silkworm and Spider Silk Proteins Revealed by Mass Photometry" https://pubs.acs.org/doi/full/10.1021/acs.jpclett.5c02335 Led by our PhD students Hannah Johnson (our lab) and Herman Dhaliwal (Garmann Lab, SDSU) — equal contributors — with expert guidance from Prof. Rees Garmann. Our team shaped the overarching questions and provided the native silk dope samples, while the Garmann lab did the heavy lifting with the mass photometry experiments.What we found: Using mass photometry (MP), we see dimers dominate in both systems, but they’re stabilized differently: • 🐛 Silkworm fibroin dimers (~690 kDa) split to ~340 kDa with DTT → consistent with disulfide-linked H–H dimers. • 🕷️ Spider MaSp dimers (~550 kDa) resist DTT → noncovalent stabilization, with evidence of MaSp1–MaSp2 heterodimers.Together, this clarifies how early oligomerization differs across silks and establishes MP as a tool for tracking higher-order assembly under spinning-relevant conditions.Huge thanks to everyone involved and DOD-AFOSR who funded the research! Convinced MP will play a major role in understanding silk formation when combined with NMR, SAXS, and modeling in an integrative structural biology framework. ...

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Acta Biomaterialia Paper on Silk Microrheology

Excited to share our latest work with Prof. Rae M. Robertson-Anderson (USD) just accepted in Acta Biomaterialia:“Local viscoelasticity of denaturing spider silk dope is governed by dynamic hierarchical intermolecular interactions”Special shout-out to the lead experimentalists:Karthik Peddireddy (Rae’s postdoc), who spearheaded the optical tweezers microrheology,Hannah Johnson (my recently graduated PhD student), who carried out the spider dissection and dope prep experiments.Together, they uncovered:A universal relaxation timescale (~0.5 s) tied to transient crosslinking,The crucial role of hierarchical assemblies in tuning local viscoelasticity,How concentration and aging reshape mechanical responses through entanglement, crosslinking, and phase separation.These results provide fresh insight into how spiders store aggregation-prone disordered proteins in their glands without premature assembly — and highlight the power of microrheology to probe hierarchical protein assemblies.Huge thanks to my collaborators and mentees for their amazing contributions!Grateful for support from the Air Force Office of Scientific Research (AFOSR) that made this work possible. https://www.sciencedirect.com/science/article/pii/S1742706125006737 ...

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Science Advances Paper on SCR Antivirals

New paper out in Science Advances: a library of synthetic carbohydrate receptors (SCRs)—small molecules that bind viral N-glycans—blocks viral entry across coronaviruses, paramyxoviruses, and filoviruses, with single-dose protection in a severe SARS-CoV-2 mouse model. Our team was a small but significant part of this: David Onofrei collected and we analyzed saturation transfer difference (STD)-NMR data to verify direct engagement of the SCR with the SARS-CoV-2 spike receptor-binding domain (RBD) in solution (see Fig. 4B). That mechanistic confirmation complements the cell and animal data and supports glycan-targeting as a broad-spectrum antiviral strategy. Proud to contribute alongside an amazing, multidisciplinary team. https://www.science.org/doi/10.1126/sciadv.ady3554 ...

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Focus Review on Spider Silk Protein LLPS

Excited to share a new focus review just published in Polymer Journal in collaboration with Thomas Scheibel’s group at the University of Bayreuth! https://fiberlab.deOver the past decade, our lab at SDSU has been investigating the structure, storage state, and assembly mechanisms of native spider silk proteins (spidroins), while the Scheibel group has led the way in producing and characterizing recombinant silk systems.This review brings those threads together!We highlight:Our joint NMR work revealing silk protein dynamics and assemblyKey differences and parallels between native and recombinant systemsA unifying framework that connects micelle formation, liquid crystal ordering, and liquid–liquid phase separation (LLPS) as a concerted, transitional process in silk fiber formation.We also discuss the practical implications of this new model for biomimetic silk spinning and future material design.Huge thanks to AFOSR for supporting this work!Check out the review: https://www.nature.com/articles/s41428-025-01039-3 ...

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New Publication in Ultramicroscopy

The lab has new paper out in Ultramicroscopy! Led by recent PhD graduate student Hannah Johnson, the paper lays out a protocol for NS-TEM of native spider silk protein micelle-like assemblies extracted directly from the spinning dope of spiders. Spider silk proteins prior to spinning are very sensitive to aggregation and preserving the native structure under EM staining conditions is challenging. Commonly used stains such uranyl acetate induce fibril formation because the stain is acidic and acidic pH is known to trigger fiber formation. By utilizing ammonium molybdate stain at pH 7, we were able to show that native silk superstructures could be preserved that closely matched our previously published cryoEM tomography data. Silk protein micelle pre-assembly is critical for fiber formation and we anticipate that this protocol will be useful for the characterization of other spider and silkworm silk dopes and those attempting to recapitulate this pre-assembly in recombinant silk systems. The published manuscript can be found here: https://www.sciencedirect.com/science/article/pii/S0304399125000233 ...

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New Langmuir Manuscript

Holland Lab has a new manuscript out in Langmuir titled: "Aspartic Acid Binding on Hydroxyapatite Nanoparticles with Varying Morphologies Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulation". The paper illustrates the significant impact nanoscale morphology has on biomolecule surface binding and organization. The study was led by recent lab PhD graduate and now lab post-doc, Yuan Li. Yuan used a bevy of SSNMR methods to structurally characterize aspartic acid adsorbed to HAP surfaces which was combined with MD simulations conducted by collaborator, Prof. Chris Lorenz @ King's College London. Excellent agreement was found between experimental SSNMR distance measurements and MD models providing atomistic-level structural insights of the bio-nano interface. This work is support by the National Science Foundation (NSF), Division of Chemistry (CHE). The paper can be found here: https://pubs.acs.org/doi/10.1021/acs.langmuir.4c02880 Yuan created some cool cover art that was published with the article: ...

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New Advanced Functional Materials Paper

The lab has a new paper out in Advanced Functional Materials titled: "Unraveling the Molecular Origin of Prey-wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR". Prey wrap spider silk exhibits high extensibility and superior toughness compared to other types of spider silk and is a promising target for biomaterials design. In this paper, the lab combines mechanical testing, solution NMR on native glands, SSNMR on spun fibers and AlphaFold structure prediction to elucidate the silk's unique liquid-to-solid transition and further correlate the silk fibers conformational structure with the silk's fantastic mechanics. These results and models are providing the fundamental basis for the design of biomimetic materials inspired by the prey wrap spider silk system. The study was led by lab post-doc, Kevin Chalek, with major contributions from David Onofrei, Julian Aldana, Hannah Johnson, and NREL scientist, Bennett Addison. For anyone interested, you can check out the paper here: Unraveling the Molecular Origin of Prey‐Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR onlinelibrary.wiley.com ...

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Holland Lab Featured in San Diego Union Tribune

In August 2023, the Holland Lab was featured in the San Diego Union Tribune. The article was on the front page of the Sunday paper! The article titled: "Rolling in the Money and Talent: SDSU Sets Up as Key Player in Science Scene" was focused on SDSU's growing research portfolio that totaled 192 M this past year. The Lab's spider silk research was featured in the article together with some nice pics of spiders and silk collection. The article can be found here: https://www.sandiegouniontribune.com/news/science/story/2023-08-27/sdsu-major-research-school ...

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