TY - UNPB
T1 - Local structural flexibility drives oligomorphism in computationally designed protein assemblies
AU - Khmelinskaia, Alena
AU - Bethel, Neville P
AU - Fatehi, Farzad
AU - Antanasijevic, Aleksandar
AU - Borst, Andrew J
AU - Lai, Szu-Hsueh
AU - Wang, Jing Yang John
AU - Mallik, Bhoomika Basu
AU - Miranda, Marcos C
AU - Watkins, Andrew M
AU - Ogohara, Cassandra
AU - Caldwell, Shane
AU - Wu, Mengyu
AU - Heck, Albert J R
AU - Veesler, David
AU - Ward, Andrew B
AU - Baker, David
AU - Twarock, Reidun
AU - King, Neil P
PY - 2023/10/19
Y1 - 2023/10/19
N2 - Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.
AB - Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.
U2 - 10.1101/2023.10.18.562842
DO - 10.1101/2023.10.18.562842
M3 - Preprint
C2 - 37905007
SP - 1
EP - 32
BT - Local structural flexibility drives oligomorphism in computationally designed protein assemblies
PB - bioRxiv
ER -