Protein Science

Cover image for Vol. 25 Issue 2

Edited By: Brian W. Matthews

Impact Factor: 2.854

ISI Journal Citation Reports © Ranking: 2014: 136/290 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

Featured

  • Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy

    Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy

    A novel 3S ΔF508 NBD1 structure demonstrates plasticity of RI and RE compared with the rest of NBD1. Stereo view of the 3S ΔF508 NBD1 structure showing either (a) 2Fo-Fc (blue, 3σ) and Fo-Fc (green, 1.5σ) density or (b) overlay of our structure (gray) with chains A (cyan) and B (green) of 2BBS. NBD1 is oriented such that the membrane spanning domain interface would be above it, and the NBD2 binding interface is opposite into the plane of the page. The F508 site is indicated as an orange sphere. ATP•Mg2+ is labeled and shown as sticks. The current structure and 2BBS are identical constructs, which crystallized in different space groups but attained the same resolution. Modeled regions of RI and RE are well supported by density and show a significant difference in their interactions with NBD1 than previously seen for human 3S ΔF508 NBD1. (c) B-factor analysis of the current structure (gray) and 2BBS chain A (cyan) and B (green) with model breaks labeled.

  • Using experimental evolution to probe molecular mechanisms of protein function

    Using experimental evolution to probe molecular mechanisms of protein function

    Sequence variants in a directed evolution. A schematic representation of sequence variants over four cycles of diversification and selection in a directed evolution. A simple 8-residue sequence is depicted with each residue indicated by a coloured circle. Wild-type residues are indicated in green and different substitute residues by other colours. At each iteration variants with the highest activity are selected (dashed ellipses) and used as a starting population for the next round of mutagenesis allowing additional mutations and further re-sampling of substituted positions. Some mutations (black circles) will be deleterious and decrease or ablate activity. As the evolution progresses positions 3 and 6 are revealed as key activity-determining residues. For simplicity and clarity only a very small fraction of possible variants are shown.

  • From invagination to navigation: The story of magnetosome-associated proteins in magnetotactic bacteria

    From invagination to navigation: The story of magnetosome‐associated proteins in magnetotactic bacteria

    Schematic model of magnetosome formation. Proteins (each is presented in a different shape or color) can be roughly divided into different stages of magnetosome formation (TM proteins cross the membrane; proteins’ sizes, shapes, colors and locations are meaningless, unless specified): (A) MamB, I, L, Q, and Y were suggested to take part in magnetosome invagination, and MamA and E in protein sorting. (B) MamK and J participate in magnetosome alignment into chains. (C) MamB, E, H, M, N, O, P, T, X, Z, and FtsZm are involved in processes such as iron transport, nucleation and chemical environment control. (D) MamC, D, G, F, R, S, Mms6 and MmsF all influence the magnetic particle size and morphology. MamC, D, G and Mms6 locations correspond to the presumed locations in the magnetosome.

  • The AbgT family: A novel class of antimetabolite transporters

    The AbgT family: A novel class of antimetabolite transporters

    Inner and outer cores of YdaH. (A) The inner core of YdaH, comprising TMs 1, 2, 5, 6 and 7 (colored red), contributes to dimerization as well as formation of a frame-like structure housing the outer core of the protomer. The outer core of YdaH is composed of TMs 3, 4, 8, 9 as well as HPs 1 and 2 (colored yellow). (B) The outer core of YdaH forms a channel (colored purple) spanning approximately from the middle of the inner membrane up to the periplasmic space. This channel was calculated using the program CAVER (http://loschmidt.chemi.muni.cz/caver). The secondary structural elements of the YdaH protomer are in yellow. Residues D180, N390, W400, P418 and D429 are in green sticks. (C) The bound Na+ (orange sphere) is found to coordinate with N390, G394, D429, N433 and a water molecule (red sphere). The Fo–Fc map, showing the bound Na+ and H2O, is contoured at 3.0 σ (blue mesh).

  • Distribution of single-nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

    Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency

    An example of common variants on a protein interface core. A: The dimeric structure of epoxide hydrolase (PDB ID: 4j03). B: The variant site (Arg287) on the dimeric interface. The mutating arginine residues are shown as orange stick models. The figure was prepared with PyMol.

  • Rational design of a monomeric and photostable far-red fluorescent protein for fluorescence imaging in vivo

    Rational design of a monomeric and photostable far‐red fluorescent protein for fluorescence imaging in vivo

    Centrosome dynamics in radial glia (RG) neural progenitors revealed by time-lapse in vivo imaging in the developing zebrafish brain. (a) A schematic shows the experimental design. (b) Representative images show that the centrosomes of RG progenitors, labeled by iBuleberry-Centrin, predominantly locate at the ventricular zone (VZ) surface. V: ventricle. Scale bar: 50 μm. (c) Representative montage of selected images from time-lapse in vivo imaging, tracking a single fluorescently labeled RG progenitor across space and time. Time “0” is defined as the time point of metaphase when the condensed chromosome is distinguishable. Minus time indicates the time before metaphase, while plus time means the time after metaphase. The mother RG progenitor undergoing division is indicated by white arrowheads, while the two daughter cells are indicated by yellow arrowheads. Arrows point to the two centrosomes in the dividing RG progenitor. Scale bar: 10 μm.

  • Binding screen for cystic fibrosis transmembrane conductance regulator correctors finds new chemical matter and yields insights into cystic fibrosis therapeutic strategy
  • Using experimental evolution to probe molecular mechanisms of protein function
  • From invagination to navigation: The story of magnetosome‐associated proteins in magnetotactic bacteria
  • The AbgT family: A novel class of antimetabolite transporters
  • Distribution of single‐nucleotide variants on protein–protein interaction sites and its relationship with minor allele frequency
  • Rational design of a monomeric and photostable far‐red fluorescent protein for fluorescence imaging in vivo

Recently Published Issues

See all

Recently Published Articles

Interactive Figures

Learn More

PROTEINS Imolecules












AuthorShelly DeForte on her recently published Protein Science paper entitled "Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree." " Read the paper here

Watch More Videos

Protein Science

Protein Science










Special Issue in Honor of Ron Levy

2015 Protein Science Best Paper Award

PROTEINS Imolecules

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.

More information can be found here.

Get access to the latest research anywhere, anytime

Download the journal app now!

SEARCH

SEARCH BY CITATION