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1. Polyclonal and monoclonal IgG binding on protein A resins-Evidence of competitive binding effects: Polyclonal and Monoclonal IgG Binding on Protein A

   https://doi.org/10.1002/bit.26286  

   Weinberg, Justin ; Zhang, Shaojie ; Crews, Gillian ; Healy, Edward ; Carta, Giorgio ; Przybycien, Todd ( August 2017 , Biotechnology and Bioengineering)
2. Taming multiple binding poses in alchemical binding free energy prediction: the β-cyclodextrin host–guest SAMPL9 blinded challenge

   https://doi.org/10.1039/D3CP02125D  

   Khuttan, Sheenam ; Azimi, Solmaz ; Wu, Joe Z. ; Dick, Sebastian ; Wu, Chuanjie ; Xu, Huafeng ; Gallicchio, Emilio ( September 2023 , Physical Chemistry Chemical Physics)

   We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force field to the SAMPL9 bCD host-guest binding free energy prediction challenge that comprises a combination of complexes formed between five phenothiazine guests and two cyclodextrin hosts. Multiple chemical forms, competing binding poses, and computational modeling challenges pose significant obstacles to obtaining reliable computational predictions for these systems. The phenothiazine guests exist in solution as racemic mixtures of enantiomers related by nitrogen inversions that bind the hosts in various binding poses, each requiring an individual free energy analysis. Due to the large size of the guests and the conformational reorganization of the hosts, which prevent a direct absolute binding free energy route, binding free energies are obtained by a series of absolute and relative binding alchemical steps for each chemical species in each binding pose. Metadynamics-accelerated conformational sampling was found to be necessary to address the poor convergence of some numerical estimates affected by conformational trapping. Despite these challenges, our blinded predictions quantitatively reproduced the experimental affinities for the beta-cyclodextrin host and, to a lesser extent, those with a methylated derivative. The work illustrates the challenges of obtaining reliable free energy data in in-silico drug design for even seemingly simple systems and introduces some of the technologies available to tackle them. 

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3. Bimolecular Binding Rates for Pairs of Spherical Molecules with Small Binding Sites

   https://doi.org/10.1137/20M1321991  

   Plunkett, Claire E. ; Lawley, Sean D. ( January 2021 , Multiscale Modeling & Simulation)

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4. Molecular origins of reduced activity and binding commitment of processive cellulases and associated carbohydrate-binding proteins to cellulose III

   https://doi.org/10.1016/j.jbc.2021.100431  

   Chundawat, Shishir P.S. ; Nemmaru, Bhargava ; Hackl, Markus ; Brady, Sonia K. ; Hilton, Mark A. ; Johnson, Madeline M. ; Chang, Sungrok ; Lang, Matthew J. ; Huh, Hyun ; Lee, Sang-Hyuk ; et al ( January 2021 , Journal of Biological Chemistry)

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5. Binding behavior of spike protein and receptor binding domain of the SARS-CoV-2 virus at different environmental conditions

   https://doi.org/10.1038/s41598-021-04673-y  

   Zhang, Meiyi ; Wang, Haoqi ; Foster, Emma R. ; Nikolov, Zivko L. ; Fernando, Sandun D. ; King, Maria D. ( December 2022 , Scientific Reports)

   Abstract A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of the COVID-19 pandemic that originated in China in December 2019. Although extensive research has been performed on SARS-CoV-2, the binding behavior of spike (S) protein and receptor binding domain (RBD) of SARS-CoV-2 at different environmental conditions have yet to be studied. The objective of this study is to investigate the effect of temperature, fatty acids, ions, and protein concentration on the binding behavior and rates of association and dissociation between the S protein and RBD of SARS-CoV-2 and the hydrophobic aminopropylsilane (APS) biosensors using biolayer interferometry (BLI) validated with molecular dynamics simulation. Our results suggest three conditions—high ionic concentration, presence of hydrophobic fatty acids, and low temperature—favor the attachment of S protein and RBD to hydrophobic surfaces. Increasing the temperature within an hour from 0 to 25 °C results in S protein detachment, suggesting that freezing can cause structural changes in the S protein, affecting its binding kinetics at higher temperature. At all the conditions, RBD exhibits lower dissociation capabilities than the full-length S trimer protein, indicating that the separated RBD formed stronger attachment to hydrophobic surfaces compared to when it was included in the S protein. 

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