Benjamin North
University of Pennsylvania
7 Papers
80 Citations
Benjamin North is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Antiparallel (biochemistry) & Protein design. The author has an hindex of 7, co-authored 7 publications. Previous affiliations of Benjamin North include Fox Chase Cancer Center.
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Papers
A new clustering of antibody CDR loop conformations
TL;DR: This work revisited the clustering of conformations of the six CDR loops with the much larger amount of structural information currently available and found that earlier predictions of "bulged" versus "nonbulging" conformations based on the presence or the absence of anchor residues Arg/Lys94 and Asp101 of H3 have not held up.
450
Computational design of a protein crystal
Christopher J. Lanci,Christopher M. MacDermaid,Seung-gu Kang,Rudresh Acharya,Benjamin North,Xi Yang,X. Jade Qiu,William F. DeGrado,Jeffery G. Saven +8 more
TL;DR: A computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals and has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.
Dn-symmetrical tertiary templates for the design of tubular proteins
TL;DR: The backbone geometries of the helical bundles of cytochrome bc(1), TolC, and DSD are well described using a simple D(n)-symmetrical model with only eight adjustable parameters, which provides an excellent starting point for construction of minimal models of these proteins as well as the de novo design of proteins with novel functions.
52
X-ray structure of a water-soluble analog of the membrane protein phospholamban : Sequence determinants defining the topology of tetrameric and pentameric coiled coils
TL;DR: A model for the pentameric form of PLB is constructed using the coiled-coil parameters derived from a single monomer in the tetrameric structure, which suggests that both buried and interfacial hydrogen bonds are important for stabilizing the parallel pentamer.
34
Characterization of a membrane protein folding motif, the Ser zipper, using designed peptides.
Benjamin North,Lidia Cristian,Xiaoran Fu Stowell,James D. Lear,Jeffrey G. Saven,William F. DeGrado +5 more
TL;DR: A peptide containing three copies of a SeraLeud heptad motif is synthesized, consistent with the designed peptide adopting either a parallel or antiparallel structure, and conformational search calculations yield the parallel dimer as the lowest energy configuration, which is significantly more stable than the parallel trimer.