Alina Sergeeva

Overview

Titles

Assistant Professor of Biochemistry and Molecular Biophysics (in Systems Biology)

Email
aps2174@cumc.columbia.edu

Lab

Barry Honig

Alina Sergeeva is an Assistant Professor affiliated with the Honig Lab. Her research focuses on molecular design across systems ranging from small molecules to large biomolecular complexes and their assemblies. She uses computational chemistry, molecular simulations, structural modeling, and protein design to understand molecular recognition and engineer molecules with new or improved properties.

Her work applies structure-based design to both basic biology and therapeutic development. In studies of neuronal connectivity, she engineers cell adhesion molecules to examine how binding affinity, specificity, stability, and cell-surface organization guide neuronal recognition, synaptic targeting, and circuit assembly. In the Fc/FcRn system, she uses free energy calculations, constant-pH simulations, and experimental validation to design antibody Fc variants with altered pH-dependent binding, with the goal of improving antibody recycling and extending antibody half-life in the bloodstream.

Together, her research combines physical chemistry, computational biophysics, bioinformatics, and protein engineering to design molecules for mechanistic discovery and biomedical applications.

Education History

PhD, Utah State University 
Theoretical and Computational Chemistry

BS, Peoples Friendship University of Russia
Chemistry

Publications

The following is a list of selected publications. Visit Alina's website for a full list.

Lee, J.H.*, Sergeeva, A.P.*, Ahlsén, G., Mannepalli, S., Bahna, F., Goodman, K.M., Xu, R., Khakh, B.S., Weiner, J.A., Shapiro, L., Honig, B. and Zipursky, S.L. (2025) Astrocyte morphogenesis requires self-recognition. Nature 644:164-172 (* indicates equal author contribution)

Sergeeva, A.P. , Katsamba, P.S., Liao, J., Sampson, J.M., Bahna, F., Mannepalli, S., Morano, N.C., Shapiro, L., Friesner, R.A. and Honig, B. (2023) Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. J. Mol. Biol. 435:168187.

Xu, S., Sergeeva, A.P. , Katsamba, P.S., Mannepalli, S., Bimela, J., Zipursky, S.L., Shapiro, L, Honig, B. and Zinn, Kai. (2022) Affinity Requirements for Control of Synaptic Targeting and Neuronal Cell Survival by Heterophilic IgSF Cell Adhesion Molecules. Cell Reports 39:110618.

Troyanovsky, R.B., Sergeeva, A.P., Indra, I., Chen, C.-S., Kato, R., Shapiro, L., Honig, B. and Troyanovsky, S.M. (2021) Sorting Of Cadherin-Catenin-Associated Proteins Into Individual Clusters. Proc. Natl. Acad. of Sci. 118:e2105550118.

Sergeeva AP,  Katsamba PS, Cosmanescu F, Brewer JJ, Ahlsen G, Mannepalli S,  Shapiro L, Honig B. DIP/Dpr interactions and the evolutionary design of specificity in protein families. Nat. Commun. 2020 11:2125.

Sergeeva AP, Popov IA, Piazza ZA, Li WL, Romanescu C, Wang LS, Boldyrev AI. Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality. Acc Chem Res. 2014 Apr 15;47(4):1349-58.

Sergeeva AP, Piazza ZA, Romanescu C, Li WL, Boldyrev AI, Wang LS. B22- and B23-: all-boron analogues of anthracene and phenanthrene. J Am Chem Soc. 2012 Oct 31;134(43):18065-73.

Zhang J, Sergeeva AP, Sparta M, Alexandrova AN. B13+: a photodriven molecular Wankel engine. Angew Chem Int Ed Engl. 2012 Aug 20;51(34):8512-5.

Sergeeva AP, Boldyrev AI. δ-Bonding in the [Pd4(μ4-C9H9)(μ4-C8H8)]+ sandwich complex. Phys Chem Chem Phys. 2010 Oct 14;12(38):12050-4.

Sergeeva AP, Boldyrev AI. Flattening a puckered pentasilacyclopentadienide ring by suppression of the pseudo Jahn-Teller effect. Organometallics. 2010;29(17):3951-3954.

Huang W, Sergeeva AP, Zhai HJ, Averkiev BB, Wang LS, Boldyrev AI. A concentric planar doubly π-aromatic B19- cluster. Nat Chem. 2010 Mar;2(3):202-6.