Protein Science

Cover image for Vol. 24 Issue 6

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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  • Structural insight into equine lentivirus receptor 1

    Structural insight into equine lentivirus receptor 1

    The overall structure of ELR1. (A) Cartoon representation of ELR1, showing a colored gradient from blue at the N-terminus (residue 40) to red at the C-terminus (residue 141). (B) Domain structure of ELR1. ELR1 is shown in a cartoon representation with CRDs 1–3 colored magenta, green and yellow, respectively. Disulfide bonds are shown as orange sticks. (C) The solvent-accessible electrostatic surface of ELR1. The surfaces are colored according to the electrostatic potential, ranging from deep blue (positive charge) to red (negative charge).

  • Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex

    Energetic evaluation of binding modes in the C3d and Factor H (CCP 19‐20) complex

    Comparison of complement response from the AP on surfaces of self (blue) and surfaces of nonself (red). (1, 4) C3b binds to both native and foreign surfaces through nucleophilic attack on an internal thioester bond. (2) On surfaces of self, FH is more likely to interact with attached C3b, preventing association with factor B and limiting the formation of the C3 convertase. In the case that C3 convertase does form, FH acts to accelerate decay of the complex. (3) Additionally, FH serves as a cofactor for conversion of attached C3b to inactive C3b that is eventually cleaved to C3d that remains surface-bound. (5) On surfaces of nonself, factor B associates with bound C3b. (6) Factor D subsequently cleaves a portion of factor B to form the C3 convertase. (7) This enzyme cleaves serum C3 into C3b, an opsonin, and C3a, an anaphylatoxin. (8) C3b generated by the convertase is capable of binding to surfaces once again and results in amplification of immune response.

  • Thermodynamic binding analysis of Notch transcription complexes from Drosophila melanogaster

    Thermodynamic binding analysis of Notch transcription complexes from Drosophila melanogaster

    Overview of CSL-mediated transcription regulation. A: Model of CSL functioning as a transcriptional switch. Left, pathway inactivity allows corepressors (CoR, magenta) to interact with CSL present on DNA in the regulatory regions of target genes, and thereby repress gene transcription. Right, when the pathway is active, the corepressor complex is exchanged for two coactivators, Notch intracellular domain (NICD, red and yellow) and Mastermind (Mam, gray) to activate transcription from Notch target genes. B: Ribbon diagram (left) and domain schematics (right) of the CSL-NICD-MAM ternary complex bound to DNA. Coloring is consistent in both images. CSL consists of three domains—NTD (cyan), BTD (green), and CTD (orange). A beta-strand that bridges all three domains of CSL is colored magenta. The NTD and BTD of CSL make contacts with the DNA (gray). The RAM domain (red) of NICD interacts solely with the BTD of CSL while the ANK domain (yellow) interacts with both the NTD and CTD of CSL. Mastermind (gray) binds as a long helix across a composite surface created by the ANK domain bound to the NTD and CTD of CSL. C: Model of ternary complex assembly. According to this model, the RAM domain (red) of NICD binds to the BTD of CSL (green) in a high affinity interaction. The ANK domain (yellow) of NICD interacts very weakly with CSL until the second coactivator, MAM (gray), is present, locking the complex into an active conformation.

  • AFN-1252 is a potent inhibitor of enoyl-ACP reductase from Burkholderia pseudomallei—Crystal structure, mode of action, and biological activity

    AFN‐1252 is a potent inhibitor of enoyl‐ACP reductase from Burkholderia pseudomallei—Crystal structure, mode of action, and biological activity

    Ribbon diagram of BpmFabI tetrameric assembly viewed down the twofold noncrystallographic axis. Each monomer along with the bound AFN-1252 is shown in a different color.

  • An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex

    An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex

    Stoichiometric differences in RAG1 to RAG2 in V(D)J recombinase complexes containing mutant versus WT core RAG1. A: Overlay of the flow cytometry data where RFP-trap beads were incubated with cell lysates coexpressing WT GFP-core RAG1 with either Ch-core-RAG2 (blue dots) or Ch-FL-RAG2 (red dots). B: Overlay of RFP-trap flow cytometry data comparing Ch-core RAG2 co-expressed with either WT (red dots) or E767K (blue dots) GFP-core RAG1. C: Relative stoichiometries of Ch-fused RAG2 to GFP-core RAG1 from representative RFP-trap flow cytometry experiments. Each point is the Cherry fluorescence signal (normalized to the Cherry signal from the coexpressed Ch-FL-RAG2:WT GFP-core RAG1 experiment) at selected GFP fluorescence signals, as illustrated in Figure S7B. Solid and dashed lines are from experiments using Ch-FL RAG2 and Ch-core-RAG2, respectively. Experiments using the different GFP-core RAG1 proteins are represented with the following symbols: WT (circles), C727,730A (diamonds), W760A,R761Q (triangles), and E767K (squares). Results from an RFP-trap experiment using co-expressed Ch-core RAG2 and GFP-core RAG1 (C727,730A) was not shown due to weak complex formation.

  • pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides

    pH responsiveness of fibrous assemblies of repeat‐sequence amphipathic α‐helix polypeptides

    Helical wheel of the α3 polypeptide. α3 was designed to be amphipathic when it formed an α-helix. Red circles show positions b and f. Polypeptides were created with substitutions of Glu at position b or Lys at position f (or both) with Ser.

  • Structure-based design of combinatorial mutagenesis libraries

    Structure‐based design of combinatorial mutagenesis libraries

    Histograms of the AMBER energies (postminimization) of structural models built for sampled variants from different complete library designs.

  • Structural insight into equine lentivirus receptor 1
  • Energetic evaluation of binding modes in the C3d and Factor H (CCP 19‐20) complex
  • Thermodynamic binding analysis of Notch transcription complexes from Drosophila melanogaster
  • AFN‐1252 is a potent inhibitor of enoyl‐ACP reductase from Burkholderia pseudomallei—Crystal structure, mode of action, and biological activity
  • An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex
  • pH responsiveness of fibrous assemblies of repeat‐sequence amphipathic α‐helix polypeptides
  • Structure‐based design of combinatorial mutagenesis libraries

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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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