Publications

High-Impact Preprints & Manuscripts in Preparation

A complete record of structural biology, molecular machines, and functional RNA research. Full citation index available on PubMed and Google Scholar.
*Denotes equal contribution.

1. Packaging a synthetic full-length HIV viral RNA into functional virions.
   Krupkin M, OhAinle M, Sundquist W, Puglisi JD, Puglisi EV.
   (Manuscript in final preparation; available upon request).

2. 4D Crystallography Captures Transient IF1-Ribosome Dynamics in Translation Initiation.
   Yapici I, Dao H, Yokoi S, Krupkin M, Puglisi EV, Puglisi JD, Wakatsuki S, DeMirci H.
   (Submitted to EMBO J).

3. Efficient HIV-1 Endogenous Reverse Transcription and Integration in a Cell-Free System.
   Christensen D, …, Krupkin M, …, Sundquist W.
   (Submitted).

Peer-Reviewed Journal Articles

1. Intelectin-2 is a broad-spectrum antimicrobial lectin.
   Dugan AE, … Krupkin M, Ribbeck K, Xavier R, Bevins C, Kiessling L.
   Nature Communications (2026). [BioRxiv Preprint]

2. A CH-π Interaction Is Required for Human Galectin-3 Function.
   Diehl RC, Chorghade JS, Keys AM, Alam MM, Early SA, Dugan AE, Krupkin M, Ribbeck K, Kulik HJ, Kiessling LL.
   JACS Au (2024). [DOI]

3. Comparison of Physicochemical Properties of Native Mucus and Reconstituted Mucin Gels.
   Wagner CE, Krupkin M, Smith-Dupont KB, Wu CM, Bustos NA, Witten J, Ribbeck K.
   Biomacromolecules (2023). [DOI]

4. Human immunodeficiency virus 1 5’-leader mutations in plasma viruses before and after the development of reverse transcriptase inhibitor-resistance mutations.
   Nouhin J, Tzou PL, Rhee SY, Sahoo MK, Pinsky BA, Krupkin M, Puglisi JD, Puglisi EV, Shafer RW.
   J Gen Virol (2023). [DOI]

5. Uncovering translation roadblocks during the development of a synthetic tRNA.
   Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnkovic A, Ehrenberg M, Puglisi EV, Söll D, Puglisi JD.
   *Nucleic Acids Res (2022). Journal Cover. [DOI]

6. Origin of life: proto ribosome forms peptide bonds and links RNA and protein dominated worlds.
   Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich AH, Peleg Y, Agmon I, Bashan A, Yonath A.
   Nucleic Acids Res (2022). Featured in Nature News. [DOI]

7. Advances in understanding the initiation of HIV-1 reverse transcription.
   Krupkin M, Jackson LN, Ha B, Puglisi EV.
   Curr Opin Struct Biol (2020). [DOI]

8. Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.
   Matzov D, Eyal Z, Benhamou RI, Shalev-Benami M, Halfon Y, Krupkin M, Zimmerman E, Rozenberg H, Bashan A, Fridman M, Yonath A.
   Nucleic Acids Res (2017). [DOI]

9. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel.
   Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A.
   Structure (2017). [DOI]

10. Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
    Krupkin M, Wekselman I, Matzov D, Eyal Z, Diskin Posner Y, Rozenberg H, Zimmerman E, Bashan A, Yonath A.
    Proc Natl Acad Sci USA (2016). [DOI]

11. A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.
    Eyal Z, Matzov D, Krupkin M, Paukner S, Riedl R, Rozenberg H, Zimmerman E, Bashan A, Yonath A.
    Sci Rep (2016). [DOI]

12. Ribosomal antibiotics: Contemporary challenges.
    Auerbach-Nevo T, Baram D, Bashan A, Belousoff M, Breiner E, Davidovich C, Cimicata G, Eyal Z, Halfon Y, Krupkin M, …, Yonath A.
    Antibiotics (Basel) (2016). [DOI]

13. Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus.
    Eyal Z, Matzov D, Krupkin M, Wekselman I, Paukner S, Zimmerman E, Rozenberg H, Bashan A, Yonath A.
    Proc Natl Acad Sci USA (2015). [DOI]

14. A recombinant collagen–mRNA platform for controllable protein synthesis.
    Sun L, Xiong Y, Bashan A, Zimmerman E, Shulman Daube S, Peleg Y, Albeck S, Unger T, Yonath H, Krupkin M, Matzov D, Yonath A.
    Chembiochem (2015). Journal Cover. [DOI]

15. Protoribosome by quantum kernel energy method.
    Huang L, Krupkin M, Bashan A, Yonath A, Massa L.
    Proc Natl Acad Sci USA (2013). [DOI]

16. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome.
    Krupkin M, Matzov D, Tang H, Metz M, Kalaora R, Belousoff MJ, Zimmerman E, Bashan A, Yonath A.
    Phil Trans R Soc B Biol Sci (2011). Research Highlight. [DOI]

17. The ribosome as drug target: lessons from 3D structures.
    Bashan A, Zimmerman E, Belousoff MJ, Rozenberg H, Davidovich C, Wekselman I, Shapira T, Krupkin M, Yonath A.
    Isr Chem Soc (2010). Journal Cover.

18. The proto-ribosome: An ancient nano-machine for peptide bond formation.
    Davidovich C, Belousoff M, Wekselman I, Shapira T, Krupkin M, Zimmerman E, Bashan A, Yonath A.
    Isr J Chem (2010). Journal Cover.

Books & Public Outreach

• Atom Structure (Forthcoming, Amazon)
  Krupkin M. (2026).
  An illustrated conceptual guide introducing young learners to atomic architecture, fundamental particles, and physical chemistry through intuitive visual models.
  Direct link to Amazon pre-order/order will be posted here upon release.

• Companion Workshop: Hands-On Atom Modeling with Clay
  Krupkin M. (2026).
  An interactive video tutorial demonstrating how to construct 3D physical models of atomic nuclei and electron shells to build early spatial intuition in structural science. Watch on YouTube.

• Book Chapter: Glimpse into the Origin of Life: What was First, the Genetic Code or its Products, the Proteins?
  Krupkin M, Bashan A, Yonath A.
  Why Does Evolution Matter? The Importance of Understanding Evolution, Cambridge Scholars Publishing, p. 87-100 (2014). [Google Books]