@article{bergman_zhang_liu_jang_nussinov_2024, title={Binding Modalities and Phase-Specific Regulation of Cyclin/Cyclin-Dependent Kinase Complexes in the Cell Cycle}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.4c03243}, abstractNote={Cyclin-dependent kinases (CDKs) are activated upon cyclin-binding to enable progression through the cell cycle. Dominant CDKs and cyclins in mammalian cells include CDK1, CDK2, CDK4, and CDK6 and corresponding cyclins A, B, D, and E. While only certain, "typical" cyclin/CDK complexes are primarily responsible for cell cycle progression, "atypical" cyclin/CDK complexes can form and sometimes perform the same roles as typical complexes. We asked what structural features of cyclins and CDKs favor the formation of typical complexes, a vital yet not fully explored question. We use computational docking and biophysical analyses to exhaustively evaluate the structure and stability of all CDK and cyclin complexes listed above. We find that binding of the complexes is generally stronger for typical than for atypical complexes, especially when the CDK is in an active conformation. Typical complexes have denser clusters, indicating that they have more defined cyclin-binding sites than atypical complexes. Our results help explain three notable features of cyclin/CDK function in the cell cycle: (i) why CDK4 and cyclin-D have exceptionally high specificity for each other; (ii) why both cyclin-A and cyclin-B strongly activate CDK1, whereas CDK2 is only strongly activated by cyclin-A; and (iii) why cyclin-E normally activates CDK2 but not CDK1. Overall, this work reveals the binding modalities of cyclin/CDK complexes, how the modalities lead to the preference for typical complexes versus atypical complexes, and how binding modalities differ between typical complexes. Our observations suggest targeting CDK catalytic actions through destabilizing their native differential cyclin interfaces.}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Bergman, Michael T. and Zhang, Wengang and Liu, Yonglan and Jang, Hyunbum and Nussinov, Ruth}, year={2024}, month={Sep} }
 @article{bang_bergman_li_mukherjee_alshehri_abbott_crook_velev_hall_you_2023, title={An integrated chemical engineering approach to understanding microplastics}, volume={1}, ISSN={["1547-5905"]}, DOI={10.1002/aic.18020}, abstractNote={AbstractEnvironmental and health risks posed by microplastics (MPs) have spurred numerous studies to better understand MPs' properties and behavior. Yet, we still lack a comprehensive understanding due to MP's heterogeneity in properties and complexity of plastic property evolution during aging processes. There is an urgent need to thoroughly understand the properties and behavior of MPs as there is increasing evidence of MPs' adverse health and environmental effects. In this perspective, we propose an integrated chemical engineering approach to improve our understanding of MPs. The approach merges artificial intelligence, theoretical methods, and experimental techniques to integrate existing data into models of MPs, investigate unknown features of MPs, and identify future areas of research. The breadth of chemical engineering, which spans biological, computational, and materials sciences, makes it well‐suited to comprehensively characterize MPs. Ultimately, this perspective charts a path for cross‐disciplinary collaborative research in chemical engineering to address the issue of MP pollution.}, journal={AICHE JOURNAL}, author={Bang, Rachel S. and Bergman, Michael and Li, Tianyu and Mukherjee, Fiona and Alshehri, Abdulelah S. and Abbott, Nicholas L. and Crook, Nathan C. and Velev, Orlin D. and Hall, Carol K. and You, Fengqi}, year={2023}, month={Jan} }
 @article{bergman_xiao_hall_2023, title={In Silico Design and Analysis of Plastic-Binding Peptides}, volume={127}, ISSN={["1520-5207"]}, DOI={10.1021/acs.jpcb.3c04319}, abstractNote={Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors.}, number={39}, journal={JOURNAL OF PHYSICAL CHEMISTRY B}, author={Bergman, Michael T. and Xiao, Xingqing and Hall, Carol K.}, year={2023}, month={Sep}, pages={8370–8381} }
 @article{harris_sikes_bergman_goller_hasley_sjogren_ramirez_gordy_2022, title={Hands-on immunology: Engaging learners of all ages through tactile teaching tools}, volume={13}, ISSN={["1664-302X"]}, url={http://dx.doi.org/10.3389/fmicb.2022.966282}, DOI={10.3389/fmicb.2022.966282}, abstractNote={Ensuring the public has a fundamental understanding of human–microbe interactions, immune responses, and vaccines is a critical challenge in the midst of a pandemic. These topics are commonly taught in undergraduate- and graduate-level microbiology and immunology courses; however, creating engaging methods of teaching these complex concepts to students of all ages is necessary to keep younger students interested when science seems hard. Building on the Tactile Teaching Tools with Guided Inquiry Learning (TTT-GIL) method we used to create an interactive lac operon molecular puzzle, we report here two TTT-GIL activities designed to engage diverse learners from middle schoolers to masters students in exploring molecular interactions within the immune system. By pairing physical models with structured activities built on the constructivist framework of Process-Oriented Guided Inquiry Learning (POGIL), TTT-GIL activities guide learners through their interaction with the model, using the Learning Cycle to facilitate construction of new concepts. Moreover, TTT-GIL activities are designed utilizing Universal Design for Learning (UDL) principles to include all learners through multiple means of engagement, representation, and action. The TTT-GIL activities reported here include a web-enhanced activity designed to teach concepts related to antibody–epitope binding and specificity to deaf and hard-of-hearing middle and high school students in a remote setting and a team-based activity that simulates the evolution of the Major Histocompatibility Complex (MHC) haplotype of a population exposed to pathogens. These activities incorporate TTT-GIL to engage learners in the exploration of fundamental immunology concepts and can be adapted for use with learners of different levels and educational backgrounds.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Harris, Felix R. and Sikes, Michael L. and Bergman, Michael and Goller, Carlos C. and Hasley, Andrew O. and Sjogren, Caroline A. and Ramirez, Melissa V. and Gordy, Claire L.}, year={2022}, month={Aug} }