Protein Science

Cover image for Vol. 24 Issue 3

Edited By: Brian W. Matthews

Impact Factor: 2.861

ISI Journal Citation Reports © Ranking: 2013: 146/291 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Enzymatic formation of a resorcylic acid by creating a structure-guided single-point mutation in stilbene synthase

    Enzymatic formation of a resorcylic acid by creating a structure‐guided single‐point mutation in stilbene synthase

    Stereo view of malonyl-CoA bound to VvSTS. The sterically important residues from the (1) CoA binding pocket (Lys 55, Arg 58 and Lys 62) are shown in purple; (2) Coumaroyl binding pocket (Ser 133, Glu 192, Thr 194, Thr 197 and Ser 338) are shown in blue; (3) Cyclization pocket (Thr 132, Met 137, Phe 215, Ile 254, Glu 256, Phe 265 and Pro 375) are shown in brown. Malonyl-CoA is labeled as MLC 390.

  • Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization

    Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization

    Overview of simulated systems: (A) monomeric native NLRP14 (light green cartoon) (B) monomeric physiological mutant NLRP14-D86V (light grey) (C) stabilized mutant NLRP14-L84R (red) (D) NLRP4 (blue) (E) dimeric native NLRP14 (light and dark green) (F) dimeric mutant NLRP14-D86V (light and dark grey).

  • Intrinsic site-selectivity of ubiquitin dimer formation

    Intrinsic site‐selectivity of ubiquitin dimer formation

    Ubiquitin dimer formation. (A) Ribbon diagram of ubiquitin showing the location of its 7 lysine residues and N- and C-termini. The translucent surface depicts electrostatic potential (blue: positive; red: negative). The image was created with the program PyMOL and PDB entry 1ubq. (B) Scheme for a chromogenic assay of ubiquitin dimer formation. Thiol–disulfide interchange between a ubiquitin variant with a C-terminal cysteine residue and an NTB mixed disulfide of a K[RIGHTWARDS ARROW]C ubiquitin variant releases NTB.

  • Crystal structure of Thermobifida fuscaCse1 reveals target DNA binding site

    Crystal structure of Thermobifida fuscaCse1 reveals target DNA binding site

    Importance of Cse1 L1 in DNA binding. (A) Structural alignment of Cse1, rotated 180° about the y-axis with reference to Figure . Zoom in highlighting L1 and the critical residues involved in DNA binding. T. fusca Cse1 (magenta); A. ferrooxidans Cse1 (yellow); T. thermophilus Cse1 (cyan). (B and C) Docking of T. fusca Cse1 into the ∼9 Å E. coli dsDNA-bound Cascade (EMD 5929) with the Cas3 density mapped from the ∼20 Å Cas3-bound dsDNA-Cascade structure (EMD 5930). (C) is rotated 120° about the y-axis with respect to (B). The crRNA or crRNA-target in pink, dsDNA in purple, Cse1 in green, Cse2 in yellow, Cas7 in gray, Cas5 in orange, Cas6e in blue, and Cas3 in light blue. Zoom in of figures depicting the interaction of the three amino acid motif and the α6 helix in L1 with (B) the target dsDNA and (C) the crRNA-target DNA, with the other components of Cascade removed. (D) EMSA comparing binding affinity by mutants of T. fusca Cse1 to the wild type. Lane 1 shows the negative control without protein, Lane 2 is the positive control using wild type (WT), subsequent lanes are the dsDNA binding affinity by the mutants. F142A, F143A, and F144A refers to alanine mutations of the specific residue, ΔGEL is the removal of the short helix which consists of G139, E140, and L141 in L1.

  • Divergent evolution of a bifunctional de novo protein

    Divergent evolution of a bifunctional de novo protein

    Rescue of ΔilvA and Δfes cells by evolved proteins Syn-I3 and Syn-F4. In each panel, the left side shows growth on rich plates supplemented with IPTG. Growth on rich plates is a control demonstrating transformation of the appropriate plasmid into the host. The right side of each panel shows transformants from the same experiment plated on minimal media supplemented with the same amount of IPTG. Growth on minimal plates demonstrates the ability of the de novo protein to rescue the conditionally essential function deleted in the host strain. Growth was observed on rich plates after 1 day. On minimal plates, growth was observed after 2 days for Δfes/Syn-F4 and ΔilvA/Syn-I3 (image taken after 6 days). No growth was observed on minimal plates with Δfes/Syn-I3 or ΔilvA/Syn-F4 after incubation for 7 days.

  • A moonlighting function of Mycobacterium smegmatis Ku in zinc homeostasis?

    A moonlighting function of Mycobacterium smegmatis Ku in zinc homeostasis?

    Model of M. smegmatis Ku illustrating the predicted zinc-binding sites. Each monomer (in purple and light pink) is modeled on template strands 1jeyA and 1jeyB. The residues previously predicted to coordinate zinc are highlighted in different colors: cysteine (red), histidine (orange), and aspartic acid (cyan). The model was created using SwissModel in automatic mode. The image was prepared with PyMOL (www.pymol.org).

  • Enzymatic formation of a resorcylic acid by creating a structure‐guided single‐point mutation in stilbene synthase
  • Intrinsic flexibility of NLRP pyrin domains is a key factor in their conformational dynamics, fold stability, and dimerization
  • Intrinsic site‐selectivity of ubiquitin dimer formation
  • Crystal structure of Thermobifida fuscaCse1 reveals target DNA binding site
  • Divergent evolution of a bifunctional de novo protein
  • A moonlighting function of Mycobacterium smegmatis Ku in zinc homeostasis?

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2015 Protein Science Best Paper Award

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We are pleased to announce the winners of the 2015 Protein Science Best Paper Award:

Chih-Chia (Jack) Su
Assistant Scientist, Biological Systems
Department of Chemistry at Iowa State University

Crystal structure of the Campylobacter jejuni CmeC outer membrane channel
Chih-Chia Su, Abhijith Radhakrishnan, Nitin Kumar, Feng Long, Jani Reddy Bolla, Hsiang-Ting Lei, Jared A. Delmar, Sylvia V. Do, Tsung-Han Chou, Kanagalaghatta R. Rajashankar, Qijing Zhang, Edward W. Yu,
Protein Sci. 23:954-961, 2014.

Minttu Virkki
Graduate Student
Department of Biochemistry and Biophysics at Stockholm University

Folding of aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core
Minttu Virkki, Nitin Agrawal, Elin Edsbacker, Susana Cristobal, Arne Elofsson, Anni Kauko
Protein Sci. 23:981-992, 2014.

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