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Mechanisms of allostery at the viral surface through the eyes of molecular simulation
Curr Opin Struct Biol. 2023 Dec 23;84:102761. doi: 10.1016/j.sbi.2023.102761. Online ahead of print.ABSTRACTThe outermost surface layer of any virus is formed by either a capsid shell or envelope. Such layers have traditionally been thought of as immovable structures, but it is becoming apparent that they cannot be viewed exclusively as static architectures protecting the viral genome. A limited number of proteins on the virion surface must perform a multitude of functions in order to orchestrate the viral life cycle, and allostery can regulate their structures at multiple levels of organization, spanning individual molecu...
Source: Current Opinion in Structural Biology - December 24, 2023 Category: Biology Authors: Firdaus Samsudin Lorena Zuzic Jan K Marzinek Peter J Bond Source Type: research

Tandem-repeat proteins conformational mechanics are optimized to facilitate functional interactions and complexations
Curr Opin Struct Biol. 2023 Dec 21;84:102744. doi: 10.1016/j.sbi.2023.102744. Online ahead of print.ABSTRACTThe architectures of tandem-repeat proteins are distinct from those of globular proteins. Individual modules, each comprising small structural motifs of 20-40 residues, are arrayed in a quasi one-dimensional fashion to form striking, elongated, horseshoe-like, and superhelical architectures, stabilized solely by short-range interaction. The spring-like shapes of repeat arrays point to elastic modes of action, and these proteins function as adapter molecules or 'hubs,' propagating signals within multi-subunit assembli...
Source: Current Opinion in Structural Biology - December 22, 2023 Category: Biology Authors: Carlos Ventura Anupam Banerjee Maria Zacharopoulou Laura S Itzhaki Ivet Bahar Source Type: research

Modelling the assembly and flexibility of antibody structures
Curr Opin Struct Biol. 2023 Dec 19;84:102757. doi: 10.1016/j.sbi.2023.102757. Online ahead of print.ABSTRACTAntibodies are large protein assemblies capable of both specifically recognising antigens and engaging with other proteins and receptors to coordinate immune action. Traditionally, structural studies have been dedicated to antibody variable regions, but efforts to determine and model full-length antibody structures are emerging. Here we review the current knowledge on modelling the structures of antibody assemblies, focusing on their conformational flexibility and the challenge this poses to obtaining and evaluating ...
Source: Current Opinion in Structural Biology - December 20, 2023 Category: Biology Authors: Dongjun Guo Maria Laura De Sciscio Joseph Chi-Fung Ng Franca Fraternali Source Type: research

Molecular simulations integrated with experiments for probing the interaction dynamics and binding mechanisms of intrinsically disordered proteins
Curr Opin Struct Biol. 2023 Dec 19;84:102756. doi: 10.1016/j.sbi.2023.102756. Online ahead of print.ABSTRACTIntrinsically disordered proteins (IDPs) exploit their plasticity to deploy a rich panoply of soft interactions and binding phenomena. Advances in tailoring molecular simulations for IDPs combined with experimental cross-validation offer an atomistic view of the mechanisms that control IDP binding, function, and dysfunction. The emerging theme is that unbound IDPs autonomously form transient local structures and self-interactions that determine their binding behavior. Recent results have shed light on whether and how...
Source: Current Opinion in Structural Biology - December 20, 2023 Category: Biology Authors: Catherine Ghosh Suhani Nagpal Victor Mu ñoz Source Type: research