Protein Science

Cover image for Vol. 24 Issue 8

Edited By: Brian W. Matthews

Impact Factor: 2.854

ISI Journal Citation Reports © Ranking: 2014: 136/289 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

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  • Structural insights into interactions between ubiquitin specific protease 5 and its polyubiquitin substrates by mass spectrometry and ion mobility spectrometry

    Structural insights into interactions between ubiquitin specific protease 5 and its polyubiquitin substrates by mass spectrometry and ion mobility spectrometry

    Molecular models of USP5 with mono-Ub bound at (A) the active site domain and (B) the ZnF-UBP domain showing the similar dimensions of the two complexes (calculated CCSs = 56.9 nm2 and 57.2 nm2, respectively).

  • Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

    Chemical cross‐linking and native mass spectrometry: A fruitful combination for structural biology

    The presentation of full-length p53 in DNA-free state in a crossshaped structure according to a previously published SAXS model. DNA-binding domain (DBD; cyan and light green) and tetramerization domain (Tet.; red) are displayed in cartoon representation, connecting linkers (gray), N-termini (salmon), and C-terminal regulatory domains (yellow) are presented in spacefill mode. The crosslinking distances (in Å) are given for the most likely crosslinked residues. It should be noted that crosslinks (numbered 1–16) are presented for both monomers M1 and M2. Right-hand side: intermolecular crosslinks (red dotted lines) in simplified representation; left-hand side: in full represenation. Reprinted with permission from Arlt C, et al., Proteomics, 2015.

  • The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes

    The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes

    Native mass spectrum of the ColE9 translocon. The inserts represent the observed species: orange hexagon, intact complex bound to a lipopolysaccharide; red circle, translocon lacking BtuB and the lipopolysaccharide; blue square, BtuB. See text for further details. This spectrum was reproduced with permission from Ref. © (2013) AAAS.

  • Conformational landscape and pathway of disulfide bond reduction of human alpha defensin

    Conformational landscape and pathway of disulfide bond reduction of human alpha defensin

    Sequence and crystal structure of human alpha defensin 5, highlighting the disulfide bridges (PDB code: 1zmp). The calculated collisional cross section (Ω) of HD5 according to the MobCal Trajectory Method is listed.

  • Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment

    Top‐down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment

    Top-down CID of membrane proteins (detergent micelles; native ESI) leads to fragmentation predominantly in membrane-embedded regions. A: Transmembrane prediction for each of the three proteins reveals potential membrane-embedded areas (red curves); comparison with observed CID fragmentation sites (black bars) shows a preference for membrane regions. B: Mapping the observed fragmentation sites onto the 3D-structures of the three membrane proteins, confirms the results obtained by TMH prediction. Peptide fragments observed are mapped (in red) onto the structures of the ion (in gray). PDB IDs 2M6X, 2OAR and 3ZRS, were respectively used for p7, MscL, and Kirbac3.1 visualization.

  • HX-MS2 for high performance conformational analysis of complex protein states

    HX‐MS2 for high performance conformational analysis of complex protein states

    Comparison of peptide scoring algorithms. (A) Intersection of peptide identifications for Mascot (applied to DDA data, P < 0.05), X!Tandem hyperscore (calculated from unique fragments in DIA data, FUR of 0.5%), and WUF score (from DIA data, FUR of 0.5%). (B) Distribution of hits as a function of peptide length, using the criteria as in (A).

  • Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly

    Electron‐capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly

    X-ray structure of hHb tetramer shown in B-factor scale (PDB code 4hhb). Top, two α-chains in color; bottom, two β-chains in color.

  • Structural insights into interactions between ubiquitin specific protease 5 and its polyubiquitin substrates by mass spectrometry and ion mobility spectrometry
  • Chemical cross‐linking and native mass spectrometry: A fruitful combination for structural biology
  • The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes
  • Conformational landscape and pathway of disulfide bond reduction of human alpha defensin
  • Top‐down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment
  • HX‐MS2 for high performance conformational analysis of complex protein states
  • Electron‐capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly

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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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