Protein Science

Cover image for Vol. 24 Issue 5

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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  • Computational de novo design of a four-helix bundle protein—DND_4HB

    Computational de novo design of a four‐helix bundle protein—DND_4HB

    Starting structures and design models. To generate starting structures for design, an initial helix bundle is assembled without loops by aligning idealized helices (rainbow with helix axis points in black) to average-normalized helical positions (large grey spheres) (A). Bridge fragments that connect adjacent helices in the bundle are identified by RMSD alignment (B) and are used with axis constraints (large grey spheres) to bias fragment assembly. Fragment assembly and flexible backbone design were used to produce the DND_4HB design model (C), where DND_4HB's axis points (small black spheres) are within 3.5 Å of the axis constraints (large grey spheres) (C). The lowest energy DND_4HB forward folding model showing that the DND_4HB sequence is optimized for a left-handed four-helix bundle but loop 3 (orange loop) may adopt an alternate conformation (D).

  • Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

    Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering

    Heatmap of average ΔSvib for pair-wise amino acid substitutions from mesophile to thermophile proteins. The top right half matrix around the inverse diagonal represent for the most part mutations that increase the stability of the thermophile protein. Missing values represent pairwise amino acid substitutions without statistically significant results. ΔSvib values are scaled by 103 for visualization purposes.

  • Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions

          Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active‐site substitutions

    R67 DHFR: The four protomers (A–D) are illustrated in red, green, blue and yellow, respectively. The active site residues 66–69 are shown in sticks representation. The linker introduced for the dimer construct and the N-terminal tail of R67 connecting protomers A,B and C,D are shown in black. The linker conformation was predicted using the loop-modelling tool of the MOE software.

  • Rapid search for tertiary fragments reveals protein sequence–structure relationships

    Rapid search for tertiary fragments reveals protein sequence–structure relationships

    Fifty structural fragments used to test the performance of MASTER. Disjoint segments are designated with cartoon color; number of segments ranged from 1 to 5, with 10 motifs considered in each category. Within a given number of segments, motifs are ordered by increasing total number of residues, in column-major fashion.

  • Design of an allosterically regulated retroaldolase

    Design of an allosterically regulated retroaldolase

    Overview of the design.

  • Computer-aided design of a catalyst for Edman degradation utilizing substrate-assisted catalysis

    Computer‐aided design of a catalyst for Edman degradation utilizing substrate‐assisted catalysis

    Model for the post-cleavage product of Edman degradation. (A) A model for the small molecule corresponding to a PITC-derivatized N-terminal alanine residue after cleavage, but before rearrangement into the phenylthiohydantoin derivative, was predicted using the quantum chemistry program GAMESS. The methyl group that corresponds to the side chain of alanine is shown in magenta. (B) The product model is shown in relation to the active site residues when modeled in complex with cruzain. The catalytic triad residues of cruzain are shown as purple sticks. In the intended catalytic mechanism for Edmanase, the sulfur atom in the PITC group takes the place of the sulfhydryl nucleophile, while the other two members of the triad (shown in black) are retained to activate the sulfur for nucleophilic attack on the N-terminal peptide bond. (C) The product analog is shown in its docked location. The mutations to cruzain are shown in magenta. The methyl group of the molecule corresponds to the side chain of an alanine residue, and is directed into solvent and away from the active site.

  • Protein unfolding rates correlate as strongly as folding rates with native structure

    Protein unfolding rates correlate as strongly as folding rates with native structure

    Correlations between structural complexity, folding and unfolding rates, and thermodynamic stability. Correlations are shown between (A) folding rates and ACO, (B) unfolding rates and ACO, (C) folding rates and LRO, (D) unfolding rates and LRO, (E) folding rates and thermodynamic stability, (F) unfolding rates and thermodynamic stability, and (G) unfolding and folding rates. The lines of best fit (solid black) and corresponding equations and correlation values are given for the whole dataset, values for subsets of data are given in Table for two-state (filled diamonds), multistate (open squares), alpha (blue), beta (red), and mixed (green) proteins. Dotted lines for panels A–D denote ±10-fold and ±100-fold variation in kf and ku, respectively.

  • Computational de novo design of a four‐helix bundle protein—DND_4HB
  • Vibrational entropy differences between mesophile and thermophile proteins and their use in protein engineering
  •       Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active‐site substitutions
  • Rapid search for tertiary fragments reveals protein sequence–structure relationships
  • Design of an allosterically regulated retroaldolase
  • Computer‐aided design of a catalyst for Edman degradation utilizing substrate‐assisted catalysis
  • Protein unfolding rates correlate as strongly as folding rates with native structure

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Video Highlight from Krishnamurthy Narasimha Rao, Anirudha Lakshminarasimhan, Sarah Joseph, Swathi U. Lekshmi, Ming-Seong Lau, Mohammed Takhi, Kandepu Sreenivas, Sheila Nathan, Rohana Yusof, Noorsaadah Abd. Rahman, Murali Ramachandra, Thomas Antony, and Hosahalli Subramanya on their recently published Protein Science paper entitled, "AFN-1252 is a potent inhibitor of enoyl-ACP reductase from Burkholderia pseudomallei—Crystal structure, mode of action, and biological activity" Read the paper here

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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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