Surfaces and High-Density Molecular Arrays (SHA)

Prof. Dr. rer. nat. Alexander Nesterov-Mueller [Contact]

Our research group combines combinatorial synthesis and high-throughput screening to explore molecular interactions and discover functional biomolecules. Our primary focus lies in studying peptides and their applications in understanding evolutionary processes, molecular recognition, and interactions with antibodies, proteins, RNA, polymers, and cells.

Our research contributes to the research program Natural, Artificial and Cognitive Information Processing (NACIP), Topic: Molecular and Cellular Information, in the research field „Information“ as defined by the Helmholtz Association. Link to NACIP website.

 

                                

The Nesterov-Mueller Research Group was founded through the ERC Starting Grant (COMBIPATTERNING, 2011–2016). Team

 

Research

Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays

Highlights:

 

  • High-throughput screening for selective RNA binders;
  • Insights into the emergence of the standard genetic code from the combinatorial fusion cascade;
  • Prediction of ancient "living" membranes.

 

See for details:  MDPI  article 

 

Scientific Chat: In the beginning, there was the code

 

See for Details:  MDPI article

 

Scientifc Chat: Origin of Life

    

Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale

Highlights:

 

  • Human peptidome library design;
  • Each antibody has a number of "non-antigenic" selective binders with sub μM affinity;
  • Simultaneous measurement of dissociation constants KD of antibodies for 6000 peptides.

 

See for details:  MDPI article

 

Scientific Chat: Off-targets of antibodies

   

Serological Number for Characterization of Circulating Antibodies

Highlights:

 

  • How to determine the number of linear and conformational monoclonal antibody epitopes in the patient's sera?
  • What causes a pre-existing antibody response after vaccination?

 

See for details: MDPI article

 

Scientific Chat: How to measure the immune system

Selective Peptide Binders to the Perfluorinated Sulfonic Acid Ionomer Nafion

Highlights:

 

  • Discovery of new functional molecules with a selective affinity for technical polymers

 

See for details: Wiley article

 

Scientific Chat: Peptides and fuel cells

High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces

Highlights:

 

  • Discovery of cell-rejection peptides in cytokines
  • Watch the video to see how cells migrate across peptide spots

 

See for details: Nature article

 

Scientific Chat: How to remove cancer cells

The Combinatorial Fusion Cascade as a Neural Network

Highlights:

 

  • From genetic code origins to novel AI architectures
  • What Is Wrong with Backpropagation?

 

See for details: MDPI article

 

Selected Publications:

  1. Nesterov-Mueller, A. The Combinatorial Fusion Cascade as a Neural Network. AI 2025, 6, 23. https://doi.org/10.3390/ai6020023

  2. Sonnentag, S.J.; Jenne, F.; Orian-Rousseau, V.; Nesterov-Mueller, A. High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces. Commun Biol 2024, 7, doi:ARTN 870 10.1038/s42003-024-06541-7

  3. Schmidt, D.; Gartner, P.; Berezkin, I.; Rudat, J.; Bilger, M.; Grünert, T.; Zimmerer, N.; Quarz, P.; Scharfer, P.; Brückel, J.; Jung, A. P.; Singh, P.; Pooja, P.; Meier, B.; Stahlberger, M.; Schabel, W.; Bräse, S.; Lanza, G.; Nesterov-Mueller, A. Selective Peptide Binders to the Perfluorinated Sulfonic Acid Ionomer Nafion. Adv Func Mater 2023, https://doi.org/10.1002/adfm.202214932

  4. Jenne, F.; Berezkin, I.; Tempel, F.; Schmidt, D.; Popov, R.; Nesterov-Mueller, A. Screening for Primordial RNA–Peptide Interactions Using High-Density Peptide Arrays. Life 2023, 13, 796. https://doi.org/10.3390/life13030796
  5. Jenne, F.; Biniaminov, S.; Biniaminov, N.; Marquardt, P.; von Bojničić-Kninski, C.; Popov, R.; Seckinger, A.; Hose, D.; Nesterov-Mueller, A. Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int. J. Mol. Sci. 2022, 23, 3515.
  6. Babii, O.; Afonin, S.; Diel, C.; Huhn, M.; Dommermuth, J.; Schober, T.; Koniev, S.; Hrebonkin, A.; Nesterov-Mueller, A.; Komarov, I.V.; Ulrich A. Diarylethene-Based Photoswitchable Inhibitors of Serine Proteases. Angew Chem Int Edit 2021, 60, 21789-21794.
  7. Nesterov-Mueller, A.; Popov, R. The Combinatorial Fusion Cascade to Generate the Standard Genetic Code. Life 2021, 11, 975. https://doi.org/10.3390/life11090975
  8. Nesterov-Müller, A.; Popov, R. Die Botschaft von LUCA — der letzte universelle gemeinsame Vorfahre. Biospektrum 2020, 26, 488–489 8 (in German).
  9. Palermo, A.; Nesterov-Mueller, A. Serological Number for Characterization of Circulating Antibodies. Int J Mol Sci 2019, 20, doi:ARTN 604
  10. Held, F.E.; Guryev, A.A.; Frohlich, T.; Hampel, F.; Kahnt, A.; Hutterer, C.; Steingruber, M.; Bahsi, H.; von Bojnicic-Kninski, C.; Mattes, D.S.; Nesterov-Mueller, A.; Marschall, M.; Tsogoeva, S.  Facile access to potent antiviral quinazoline heterocycles with fluorescence properties via merging metal-free domino reactions. Nat Commun 2017, 8, doi:ARTN 15071
  11. von Bojnicic-Kninski, C.; Popov, R.; Dorsam, E.; Loeffler, F.F.; Breitling, F.; Nesterov-Mueller, A. Combinatorial Particle Patterning. Adv Funct Mater 2017, 27, doi:ARTN 1703511
  12. Nesterov-Müller, A.: Erfolgreicher Grenzgang : Bunsen und Kirchhoff: Entdeckung der Spektralanalyse, Physik in unserer Zeit 2016, 47: 233–237, DOI: 10.1002/piuz.201601440 (in German).
  13. Popova, A.A.; Schillo, S.M.; Demir, K.; Ueda, E.; Nesterov-Mueller, A.; Levkin, P.A. Droplet-Array (DA) Sandwich Chip: A Versatile Platform for High-Throughput Cell Screening Based on Superhydrophobic-Superhydrophilic Micropatterning. Adv Mater 2015, 27, 5217-5222, doi:10.1002/adma.201502115.
  14. Maerkle, F.; Loeffler, F.F.; Schillo, S.; Foertsch, T.; Muenster, B.; Striffler, J.; Schirwitz, C.; Bischoff, F.R.; Breitling, F.; Nesterov-Mueller, A. High-Density Peptide Arrays with Combinatorial Laser Fusing. Adv Mater 2014, 26, 3730-3734, doi:10.1002/adma.201305759.