Protein Science

Cover image for Vol. 26 Issue 10

Edited By: Brian W. Matthews

Impact Factor: 2.523

ISI Journal Citation Reports © Ranking: 2016: 158/286 (Biochemistry & Molecular Biology); 160/290 (BIOCHEMISTRY & MOLECULAR BIOLOGY)

Online ISSN: 1469-896X

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  • Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae

    Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae

    Structure of the catalytic domain of budding yeast Cdc14p. (A) The electron density of the Swi6p phosphopeptide bound to Cdc14p. The omit FO–FC map covering the Swi6p phosphopeptide is shown in blue mesh (contoured at 3.0σ) with the refined model of the Swi6p phosphopeptide. (B) Superposition of budding yeast Cdc14p (green) and human Cdc14B (orange; PDB code, 1OHE). (C) Two orthogonal views showing the overall structure of the catalytic domain of budding yeast Cdc14p (C283S; ribbon representation) bound to the Swi6p phosphopeptide (stick representation). The A- and B-domains are colored blue and green, respectively. The linker helix connecting the A- and B-domains is colored purple. The C-terminal extension is colored orange. (D) Primary structure of the catalytic domain of Cdc14p, with secondary structure assignment. (E) A stereo view of the interactions between Cdc14p (ribbon representation) and the Swi6p phosphopeptide (stick representation with yellow carbons) at the substrate-binding cleft formed at the interface of the A-domain (blue) and the B-domain (green). The Cdc14p residues that are involved in the recognition of the phosphopeptide substrate are shown in stick representation with orange carbons. Dashed lines represent hydrogen bonds or salt bridges.

  • Neutron crystallographic studies of T4 lysozyme at cryogenic temperature

    Neutron crystallographic studies of T4 lysozyme at cryogenic temperature

    Nuclear density maps of d-wt*T4L. (A) Salt bridge between His31-Asp70. (B) An unusual interaction between Ser117 and Asn132. Glu45symm is shown in magenta. (C) Hydrogen bonds network around Thr157. (D) Stereo view of two water molecules in Cavity 1. (E) Stereo view of the water molecule in Cavity 2. The nuclear density 2|Fo|-|Fc| maps are in grey, contoured at 1.0 r.m.s.d. Omit nuclear density |Fo|-|Fc| maps are in red, contoured at 1.8 r.m.s.d

  • Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain

    Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain

    Both CsgD dimerization interfaces are crucial for curli production examined by Congo red assay. A. Congo red agar assay experiment of WT, CsgD knockout, pBAD empty vector, pBADCsgD, K18A, L21AQ22A, D59A, E62A, Q88A, and I140A strains in Salmonella Typhimurium IR715 background. The red color degree serves as a surrogate for the amount of curli production. B. Congo red assay of planktonic cell using the same strains as panel A. The Congo red absorption of all strains were quantified and normalized by cell density (OD490/OD600). The tubes picture on the right indicated the pBAD empty vector and pBADCsgD strains. Data are cell density value means ± SD of 5–7 replicates.

  • Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies

    Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies

    Schematic diagrams of various BsAb modalities. The top left are schematics of two monoclonal IgGs with their unique antigen-binding regions colored red and blue. Each Ig-fold domain is depicted as an oval. The LCs comprising VL and CL could be κ or λ isotype. The top right depicts examples of domain or Fv based BsAbs. The center panel depicts commonly employed IgG-like BsAbs that use IgG or IgG-Fc to impart IgG-like pharmacokinetics combined with antibody fragments to enable bispecific binding. The bottom panel depicts two different fully IgG BsAb modalities. The work described in this report focuses on the generation of monovalent IgG BsAbs as depicted on the left in the blue square.

  • Defining the metal specificity of a multifunctional biofilm adhesion protein

    Defining the metal specificity of a multifunctional biofilm adhesion protein

    Hydrodynamic modeling of Brpt1.5 and Brpt5.5. Brpt1.5 crystal structures were used for hydrodynamic modeling of monomer and dimer species. (A) A low-resolution bead model of the Brpt1.5 monomer is created from the coordinates of each crystal structure and combined into an ensemble used to predict the average sedimentation coefficient and frictional ratio. (B) Structures of the Zn2+-induced Brpt1.5 dimer were used to create a bead model to estimate the sedimentation parameters of a homogenous Brpt1.5 dimer population. (C) Since no structure of Brpt5.5 has currently been solved, various Brpt1.5 structures were combined to create an ensemble of homology models for the longer construct, yielding predicted sedimentation parameters that were similar to experimental values.

  • Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type

    Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type

    Ribbon diagram of the T26H mutant showing its two-domain structure. The side-chains of acidic (Asp and Glu) and basic (Arg, His and Lys) residues are shown with sticks and colored in pink and blue, respectively. The active site residues Glu11, Asp20 and His26 in the cleft are indicated in bold letters. Further amino acid residues described in the text are labeled.

  • Structure and dimerization of the catalytic domain of the protein phosphatase Cdc14p, a key regulator of mitotic exit in Saccharomyces cerevisiae
  • Neutron crystallographic studies of T4 lysozyme at cryogenic temperature
  • Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain
  • Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies
  • Defining the metal specificity of a multifunctional biofilm adhesion protein
  • Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type

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Author Suzanne Scarlata on her recently published Protein Science paper entitled "Regulation of the Activity of the Promoter of RNA-induced Silencing, C3PO." Read the paper here

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2017 Best Paper Award Winners
We are pleased to announce the winners of the 2017 Protein Science Best Paper Award:

Charlotte Miton
Postdoctoral Research Fellow
Michael Smith Laboratories at University of British Columbia

How mutational epistasis impairs predictability in protein evolution and design
Charlotte M. Miton and Nobuhiko Tokuriki
Protein Sci. 25:1260-1272, 2016.

Zach Schaefer
Graduate Student
Department of Biochemistry and Molecular Biology at University of Chicago

A polar ring endows improved specificity to an antibody fragment
Zachary P. Schaefer, Lucas J. Bailey and Anthony A. Kossiakoff
Protein Sci. 25:1290-1298, 2016.

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2017 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 2017 winner is Dr. David Pagliarini (University of Wisconsin, Madison).

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More information on our awards can be found here.

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