Protein Science

Cover image for Vol. 25 Issue 7

Edited By: Brian W. Matthews

Impact Factor: 3.039

ISI Journal Citation Reports © Ranking: 2015: 118/289 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • A polar ring endows improved specificity to an antibody fragment

    A polar ring endows improved specificity to an antibody fragment

    A: Crystal structure of triple aspartate mutant 11E H3L3 in complex with Asf1. B: Aromatic CDR H3 residues (green) comprising both the energetic and aggregation hotspot form intimate contacts with Asf1 (blue). T100bD is directly adjacent to hotspot residues while W100d is buried within the Fab scaffold. C: Location of three substitute aspartate residues in 11E H3L3 forming a cluster projecting outward from Asf1.

  • Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5

    Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5

    Structure of a TRAF-peptide complex (PDB ID 1L0A). (A) Structure of TRAF3 (teal) bound to the TRAF interaction motif (TIM) from TANK (shown in sticks) with the peptide core site and exosite-binding region used in the SiteMAP analysis highlighted in blue and gold, respectively. (B) The five residues corresponding to the core motif (PIQCT) of TANK are shown in stick representation (blue) in the TRAF3 binding groove (teal).

  • Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases

    Artificial domain duplication replicates evolutionary history of ketol‐acid reductoisomerases

    Cartoon representations of the class I KARI dimer (left) and class II KARI monomer (right), illustrating the figure-of-eight knot, the duplication of the knotted domain, and the fact that the substrate makes contact with the Rossmann domain as well as components of both knotted domains.

  • Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

    Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

    Potential use of experimental fitness maps to interpret polymorphisms observed in natural populations. The top panel illustrates potential DNA sequences from 10 individuals in a population. In these 10 theoretical sequences there are three polymorphisms that cause amino acid changes in the encoded protein. Interpreting the potential impact of polymorphism on fitness and health is a major challenge in the genomic era. Fitness maps from mutational scanning as theoretically illustrated in the bottom panel could be a powerful approach to interpret the impacts of polymorphisms in humans and other natural populations.

  • Classification of proteins with shared motifs and internal repeats in the ECOD database

    Classification of proteins with shared motifs and internal repeats in the ECOD database

    Motifs within divergent folds. The P-loop domains-related H-group includes two T-groups colored according to secondary structural element, with the P-loop in magenta. α-helices are in cyan and β-sheets in yellow, with any remaining regions in gray. (A) The P-loop containing nucleoside triphosphate hydrolases exemplified by Guanylate Kinase (e4qrhA1) has a main α/β/α core topology with five parallel β-strands, while the (B) PEP carboxykinase-like group exemplified by HPr kinase/phosphatase has a β-strand core that wraps into an open barrel with α-helices flanking one side. The β-hammerhead motif (magenta) unifies the α/β-hammerhead/Barrel-sandwich hybrid H-group including (C) the all-β single-hybrid motif (e1dczA1), and (D) the α/β-hammerhead (e1brwA2).

  • Why reinvent the wheel? Building new proteins based on ready-made parts

    Why reinvent the wheel? Building new proteins based on ready‐made parts

    Conserved catalytic machinery on widely different active-site backbones (A) Two members of the amidohydrolase family: phosphotriesterase (PTE, magenta) and lactonase (PLL, cyan) have remarkably conserved core catalytic groups, comprising two metal ions (green spheres) and chelating residues (sticks). (B) Divergence of the active-site loops leads to quite different binding sites of PTE (C) and PLL (D). Substrates shown as sticks and protein in surface. Molecular representations were generated using PyMol [The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.].

  • Selection on protein structure, interaction, and sequence

    Selection on protein structure, interaction, and sequence

    Aspects of protein biochemistry/biophysics on which selective pressures may act are depicted. (1) Stability of the folded state; (2) protein aggregation; (3) misfolding and kinetic traps; (4) nonspecific binding or change in the binding partner at the native site; (5) binding at a new site; (6) concentration levels of the protein; (7) kinetic motions of the protein. Images obtained from the RSCB PDB (www.rscb.org) of PDB ID 2MRK, PDB ID 1KA5, and Foldit.

  • A polar ring endows improved specificity to an antibody fragment
  • Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5
  • Artificial domain duplication replicates evolutionary history of ketol‐acid reductoisomerases
  • Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature
  • Classification of proteins with shared motifs and internal repeats in the ECOD database
  • Why reinvent the wheel? Building new proteins based on ready‐made parts
  • Selection on protein structure, interaction, and sequence

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Special Issue in Honor of Ron Levy

Protein Science Awards

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2016 Best Paper Award Winners
We are pleased to announce the winners of the 2016 Protein Science Best Paper Award:

Tracy Clinton
Air Force Biochemist

Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets
Tracy R. Clinton, Matthew T. Weinstock, Michael T. Jacobsen, Nicolas Szabo-Fresnais, Maya J. Pandya, Frank G. Whitby, Andrew S. Herbert, Laura I. Prugar, Rena McKinnon, Christopher P. Hill, Brett D. Welch, John M. Dye, Debra M. Eckert and Michael S. Kay
Protein Sci. 24:446-463, 2015.

Michael Thompson
Postdoctoral Fellow
Department of Bioengineering and Therapeutic Sciences at University of California, San Francisco

An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein
Michael C. Thompson, Duilio Cascio, David J. Leibly and Todd O. Yeates
Protein Sci. 24:956-975, 2015.

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2016 Young Investigator Award Winner

The Protein Science Young Investigator Award recognizes a scientist generally within the first 8 years of an independent career who has made an important contribution to the study of proteins. The 2016 winner is Dr. Benjamin Garcia (University of Pennsylvania Perelman School of Medicine).

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More information on our awards can be found here.

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