Institute of Fundamental Technological Research
Polish Academy of Sciences


Joseph Baker

The College of New Jersey (US)

Recent publications
1.  Moreira R., Vargas Guzman H., Boopathi S., Baker J.L., Poma Bernaola A., Characterization of structural and energetic differences between conformations of the SARS-CoV-2 spike protein, Materials, ISSN: 1996-1944, DOI: 10.3390/ma13235362, Vol.13, No.23, pp.5362-1-14, 2020

The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2.

COVID-19, SARS-CoV-2, spike protein, RBD, structural stability, large conformational changes, protein complexes, free energy, molecular dynamics, dynamics contact analysis

Moreira R. - IPPT PAN
Vargas Guzman H. - Max-Planck-Institute for Polymer Research (DE)
Boopathi S. - other affiliation
Baker J.L. - The College of New Jersey (US)
Poma Bernaola A. - IPPT PAN
2.  Moreira R., Chwastyk M., Baker J.L., Vargas Guzman H.A., Poma A., Quantitative determination of mechanical stability in the novel coronavirus spike protein, NANOSCALE, ISSN: 2040-3364, DOI: 10.1039/D0NR03969A, Vol.12, No.31, pp.16409-16413, 2020

We report on the novel observation about the gain in mechanical stability of the SARS-CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our findings have several biological implications in the subfamily of coronaviruses, as they suggest that the receptor binding domain (RBD) (~200 amino acids) plays a fundamental role as a damping element of the massive viral particle's motion prior to cell-recognition, while also facilitating viral attachment, fusion and entry. The mechanical stability via pulling of the RBD is 250 pN and 200 pN for CoV2 and CoV1 respectively, and the additional stability observed for CoV2 (~50 pN) might play a role in the increasing spread of COVID-19.

Moreira R. - IPPT PAN
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Baker J.L. - The College of New Jersey (US)
Vargas Guzman H.A. - Max-Planck-Institute for Polymer Research (DE)
Poma A. - IPPT PAN

List of chapters in recent monographs
Moreira R.A., Baker J.L., Guzman H.V., Poma A.B., Computer Simulations of Aggregation of Proteins and Peptides, Methods in Molecular Biology, rozdział: Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations, Springer, 2340, pp.357-378, 2022

Conference abstracts
1.  Bogin B., Fairfield M., Goncalves R., Jarquin K., Jones S., Lovenduski C., Marin K., Webb E., Vargas H., Poma Bernaola A., Biais N., Baker J.L., Filaments under force: a computational molecular-scale investigation of type IV Pili from multiple organisms, 65th Annual Meeting of the Biophysical Society, 2021-02-22/02-26, virtual meeting (US), DOI: 10.1016/j.bpj.2020.11.1886, pp.294a, 2021

Type IV pili (T4P) are biopolymers comprised of many protein subunits called pilin. These pilin subunits are not covalently bonded to one another, however remarkably T4P filaments are very strong and flexible. T4P emanate from the surface of prokaryotic cells and are utilized for many functions, including biofilm formation, surface adhesion, motility, and infection. The recent cryo-EM based structures for T4P from Escherichia coli, Neisseria meningitidis, Pseudomonas aeruginosa, and Neisseria gonorrhoeae have provided unprecedented insights into the structures of these filaments. However, although the structures of T4P are known, the dynamics of these filaments at the molecular scale at equilibrium and under tensile forces is not well characterized. In this work we provide an overview of our research into these various T4P filaments and their constituent pilin monomers under force. Specifically we carried out steered molecular dynamics simulations using a multiscale approach encompassing all-atom simulations and two levels of coarse-grained simulation. We have analyzed the changes in secondary structure of pilin subunits, global changes in filament architecture, and calculated the Young's modulus of each of the different T4P filaments. By drawing comparisons between all of these filament systems, we are able to obtain a broader picture of T4P dynamics than experimental structures alone can provide. In particular, we observe elongation of the alpha helix region of pilin subunits in each of these systems, which has been previously attributed to T4P flexibility and strength.

filament, molecular dynamics, coarse graining, T4P

Bogin B. - other affiliation
Fairfield M. - other affiliation
Goncalves R. - other affiliation
Jarquin K. - other affiliation
Jones S. - other affiliation
Lovenduski C. - other affiliation
Marin K. - other affiliation
Webb E. - other affiliation
Vargas H. - other affiliation
Poma Bernaola A. - IPPT PAN
Biais N. - other affiliation
Baker J.L. - The College of New Jersey (US)

Category A Plus


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