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1. Structural motifs in protein cores and at protein–protein interfaces are different

   https://doi.org/10.1002/pro.3996  

   Hadarovich, Anna; Chakravarty, Devlina; Tuzikov, Alexander V.; Ben‐Tal, Nir; Kundrotas, Petras J.; Vakser, Ilya A. (November 2020, Protein Science)

   Abstract Structures of proteins and protein–protein complexes are determined by the same physical principles and thus share a number of similarities. At the same time, there could be differences because in order to function, proteins interact with other molecules, undergo conformations changes, and so forth, which might impose different restraints on the tertiary versus quaternary structures. This study focuses on structural properties of protein–protein interfaces in comparison with the protein core, based on the wealth of currently available structural data and new structure‐based approaches. The results showed that physicochemical characteristics, such as amino acid composition, residue–residue contact preferences, and hydrophilicity/hydrophobicity distributions, are similar in protein core and protein–protein interfaces. On the other hand, characteristics that reflect the evolutionary pressure, such as structural composition and packing, are largely different. The results provide important insight into fundamental properties of protein structure and function. At the same time, the results contribute to better understanding of the ways to dock proteins. Recent progress in predicting structures of individual proteins follows the advancement of deep learning techniques and new approaches to residue coevolution data. Protein core could potentially provide large amounts of data for application of the deep learning to docking. However, our results showed that the core motifs are significantly different from those at protein–protein interfaces, and thus may not be directly useful for docking. At the same time, such difference may help to overcome a major obstacle in application of the coevolutionary data to docking—discrimination of the intramolecular information not directly relevant to docking. 

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2. Effects of SARS‐CoV‐2 mutations on protein structures and intraviral protein–protein interactions

   https://doi.org/10.1002/jmv.26597  

   Wu, Siqi; Tian, Chang; Liu, Panpan; Guo, Dongjie; Zheng, Wei; Huang, Xiaoqiang; Zhang, Yang; Liu, Lijun (April 2021, Journal of Medical Virology)

   null (Ed.)
3. Biotechnological and protein-engineering implications of ancestral protein resurrection

   https://doi.org/10.1016/j.sbi.2018.02.007  

   Risso, Valeria A; Sanchez-Ruiz, Jose M; Ozkan, S Banu (August 2018, Current Opinion in Structural Biology)
4. Characterizing protein–surface and protein–nanoparticle conjugates: Activity, binding, and structure

   https://doi.org/10.1063/5.0101406  

   Correira, Joshua M.; Handali, Paul R.; Webb, Lauren J. (September 2022, The Journal of Chemical Physics)

   Many sensors and catalysts composed of proteins immobilized on inorganic materials have been reported over the past few decades. Despite some examples of functional protein–surface and protein–nanoparticle conjugates, thorough characterization of the biological–abiological interface at the heart of these materials and devices is often overlooked in lieu of demonstrating acceptable system performance. This has resulted in a focus on generating functioning protein-based devices without a concerted effort to develop reliable tools necessary to measure the fundamental properties of the bio–abio interface, such as surface concentration, biomolecular structure, and activity. In this Perspective, we discuss current methods used to characterize these critical properties of devices that operate by integrating a protein into both flat surfaces and nanoparticle materials. We highlight the advantages and drawbacks of each method as they relate to understanding the function of the protein–surface interface and explore the manner in which an informed understanding of this complex interaction leads directly to the advancement of protein-based materials and technology. 

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5. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions

   https://doi.org/10.1016/j.celrep.2023.113229  

   Nandana, Vidhyadhar; Rathnayaka-Mudiyanselage, Imalka W; Muthunayake, Nisansala S; Hatami, Ali; Mousseau, C Bruce; Ortiz-Rodríguez, Luis A; Vaishnav, Jamuna; Collins, Michael; Gega, Alisa; Mallikaarachchi, Kaveendya S; et al (October 2023, Cell Reports)