Protein Science

Cover image for Vol. 24 Issue 7

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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  • Eliminating antibody polyreactivity through addition of N-linked glycosylation

    Eliminating antibody polyreactivity through addition of N‐linked glycosylation

    Design of N-linked glycan mutants. Top-left: polyreactive-enhancing residues (colored in red) for each of the three VRC07 variants (W54HC for VRC01-av1, Light chain AAAA N terminus for VRC07-av2, and R43LC for VRC07-av3). Top-right: residues positions to introduce N-linked glycans for VRC07-av1. Bottom left: residues positions to introduce N-linked glycans for VRC07-av3. Bottom right: residues positions to introduce N-linked glycans for VRC07-av2. The polyreactive-enhancing residues and the positions where the N-linked glycans were designed are colored red and yellow, respectively. The distances between the Cβ atoms of polyreactive-enhancing residues (W54HC, R43LC, and A3LC, respectively) and the designed glycans are labeled (in Å).

  • Cryo-EM structure of fatty acid synthase (FAS) from Rhodosporidium toruloides provides insights into the evolutionary development of fungal FAS

    Cryo‐EM structure of fatty acid synthase (FAS) from Rhodosporidium toruloides provides insights into the evolutionary development of fungal FAS

    Architecture and domain organization of fungal FAS I. Fungal FAS I is an overall D3 symmetric barrel-shaped complex of homohexameric or heterodocameric (α6β6) oligomerization. For clarity of the structure representation, the protein is abstracted as a cross-section along the threefold axis. Fatty acid synthesis proceeds in two compartments, each of which is lined by three full sets of catalytic domains. The positioning of a set of domains is indicated for the upper compartment. The domains ketoacyl synthase (KS), ketoacyl reductase (KR), and phosphopantetheine transferase (PPT) comprise the central wheel part, while the other domains, acetyl-transferase (AT), enoyl reductase (ER), dehydratase (DH), and malonyl-palmitoyl-transferase (MPT) make up the dome-like structure. Fungal FAS I can be encoded by a single gene, as in the case of the group of Ustilaginomcetes, or split into two separate genes (FAS1 encoding the β-chain and FAS2 encoding the α-chain) as indicated. A mobile acyl carrier protein (ACP) as a single (n = 1) or duplicated domain (n = 2) spans the inner volume of the compartments, tethered by flexible linkers to the center of the wheel and the wall of the dome (abstracted by gray lines).

  • An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein

    An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein

    Crystal structure of EutL from Clostridium perfringens (CpEutL)(this work), colored as in Figure but with the β3–β4 loops colored green, and the β7–β8 loops colored cyan. Three symmetry-related copies of each of these two loops pack tightly at the center of the trimer, resulting in a conformation that is essentially closed to transport. Three conserved amino acids that appear to be important for stabilizing this closed conformation (Y69, N74, N183) are shown as sticks.

  • Biophysical characterization of naturally occurring titin M10 mutations

    Biophysical characterization of naturally occurring titin M10 mutations

    Model of M10 domain of titin (green) bound to OL1 of obscurin-like-1 (gray), adapted from. Amino acid sequence with numbering system used shown at the bottom. Finnish mutation (37EVTW [RIGHTWARDS ARROW] VKEK) is colored blue, Italian mutation (H56 [RIGHTWARDS ARROW] P) is colored yellow, Belgian mutation (I57 [RIGHTWARDS ARROW] N) is colored red, and French mutation (L66 [RIGHTWARDS ARROW] P) is colored orange.

  • Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

    Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase

    Overlay of the binary (1LJ8; orange) and ternary (1M2W; dark blue) structures of pfMDH where no large structural rearrangement occurs when d-mannitol is bound. (A) The structures have a Cα-RMSD of 0.7 Å. NAD is shown in spheres and d-mannitol is depicted in teal. (B) Active site overlay of the binary and ternary structures of pfMDH. There is no substantial conformational change in active site residues between the binary and ternary structures. Hydrogen bonds between 1LJ8 and d-mannitol are shown in green while interactions between 1M2W and d-mannitol are shown in purple. The C2 carbon of d-mannitol is shown in yellow and water is represented as spheres. (C) Rear projection of Figure (B). Figures were made with PyMol version 1.703.

  • On the lack of polymorphism in Aβ-peptide aggregates derived from patient brains

    On the lack of polymorphism in Aβ‐peptide aggregates derived from patient brains

    In vivo (three-fold symmetry) and in vitro (three-fold and two-fold symmetry) ssNMR structural models of Aβ40 fibrils. (a) The three-fold in vivo Aβ40 fibrils model (PDB code 2M4J) with the entire residues 1–40 structurally ordered. Six strands within the strand–loop–strand units are shown. The three strand–loop–strand units are colored blue, green, or black for clarification. The side chains of D23 (red) and K28 (magenta) form a salt bridge (indicated with an arrow). (b) The three-fold in vitro model, consisting of three strand–loop–strand structures (PDB codes 2LMP) with six strands (repeats) within the strand–loop–strand motifs. The three strand–loop–strand units are colored blue, green, or black for clarification. Only residues 9–40 are shown. (c) The two-fold in vitro Aβ40 fibril model, consisting of two strand–loop–strand structures with nine strands (2LMO). The side chains of D23 (red) and K28 (magenta) form a salt bridge (indicated with an arrow). Residues 9–40 are shown in which the β-sheets are associated through C-terminal-to-C-terminal interfaces. The two strand–loop–strand units are colored blue and green. In all models, we display hydrophobic contacts between F19 (red color) and L34 (yellow color) in each strand–loop–strand units as spheres. The I32 and V40 form contacts between different cross-β units in the in vivo three fold aggregate; similar contacts are formed in the in vitro three-fold conformer between I31 and V39 (shown as spheres). The in vivo three fold also forms contacts between the side chain of R5 and V24 adjacent layers; while in the in vitro three fold it involves H13 and V40 (shown as spheres in brown color). The hydrophobic cavity is formed by residues M35 and V40 for the three-fold in vivo model and M35 for the in vitro model (shown gray spheres)

  • How do disordered regions achieve comparable functions to structured domains?

    How do disordered regions achieve comparable functions to structured domains?

    The level of disorder in proteins can vary greatly, even within what is traditionally considered a “structured domain” and a “disordered region.” Both structured domains and disordered regions are fundamental units of protein function, and most eukaryotic proteins are composed of both types of region. Reprinted with permission from Babu et al., Science, 2012, 337, 1460–1461, © American Association for the Advancement of Science.

  • Eliminating antibody polyreactivity through addition of N‐linked glycosylation
  • Cryo‐EM structure of fatty acid synthase (FAS) from Rhodosporidium toruloides provides insights into the evolutionary development of fungal FAS
  • An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein
  • Biophysical characterization of naturally occurring titin M10 mutations
  • Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase
  • On the lack of polymorphism in Aβ‐peptide aggregates derived from patient brains
  • How do disordered regions achieve comparable functions to structured domains?

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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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