Protein Science

Cover image for Vol. 26 Issue 7

Edited By: Brian W. Matthews

Impact Factor: 2.523

ISI Journal Citation Reports © Ranking: 2016: 158/286 (Biochemistry & Molecular Biology)

Online ISSN: 1469-896X

Featured

  • Proteins mediating DNA loops effectively block transcription

    Proteins mediating DNA loops effectively block transcription

    LacI bound to an O1 operator pauses transcription. (A) A schematic representation of the DNA template used in magnetic tweezer transcription assays. The template contained a T7A1 promoter close to the upstream end, a stall site at position +22, an O1 operator, the lambda t1 terminator (λt1) and a biotin label at the downstream end. A streptavidin-labeled paramagnetic bead was coupled to the biotin label to for micromanipulation in the magnetic tweezer. Four examples of transcriptional elongation recorded using the magnetic tweezers are displayed. In (B) no LacI was included and transcription shortened the DNA tether progressively without interruption. When LacI was included (C–E), transcription shortened the tether by about 0.2 um before pausing for about 200 s and then resuming. Transcription finally ceased after the tether shortened by either 0.35 um (C and D), a distance corresponding to the location of a terminator sequence, or 0.5 um (B and E), a distance corresponding to the end of the template.

  • Single-molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase

    Single‐molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase

    Single-stranded nucleic acid-dependent conformational changes of NS3h. A: Structural alignment of NS3-ssRNA and NS3h-ssDNA (PDB ID: 3O8C, 3KQH, respectively). Carbons of ssRNA and ssDNA are colored in cyan and orange accordingly, other atoms are colored by atom type (dark blue, nitrogen; red, oxygen; tan, phosphate). Residues 487 to 623 of domain 3 (D3) were used for the structural alignment. The scale bar shows the calculated Qres values, which indicate structural similarity. B: Local conformational and interaction changes of the single-stranded nucleic acid in complex with NS3/NS3h. The sidechain and backbone atoms of NS3/NS3h residues that interact with nucleotides are shown with sticks and are labeled with different colors (black dashed lines refer to the same interacting residues between NS3–ssRNA and NS3h–ssDNA; cyan dashed lines refer to uniquely interacting residues in the NS3–ssRNA structure; orange dashed lines show interactions in the NS3h–ssDNA structure). Motif V (residues 410 to 419) of NS3–ssRNA (cyan) and NS3h–ssDNA (orange) are shown as cartoon coils. Nucleotide residues (NA1 to NA5) and the 5′ and 3′ ends of the strands are labeled. C: Surface charge distribution of NS3h–ssDNA complex. The accessible surface of NS3h–ssDNA is colored based on electrostatic potentials (positive charge, blue; negative charge, red; neutral, white). The molecular view with D1 and D2 on the bottom, and the D3 on the top is similar to that in (A). The reverse side of the NS3h–ssDNA complex is shown in (D). The electrostatic surface was calculated using the program VMD with APBS plugin.

  • Molecular stretching modulates mechanosensing pathways

    Molecular stretching modulates mechanosensing pathways

    (A) Illustration of the domain structure of full-length talin. The talin head domain contains a FERM domain (50 kDa), followed by a flexible “neck” (10 kDa) which connects the head domain to its C-terminal rod domain (220 kDa). The rod domain contains 11 cryptic VBS (drawn in blue). The dimerization domain is a single helix that sits at the end of the rod. (B) Schematics of the talin structure and interaction of the talin dimer with vinculin in cells. A. Illustration of the domain structure of full-length talin. Talin head domain contains a FERM domain (50 kDa), followed by a flexible “neck” (10 kDa), which connects the head domain to its C-terminal rod domain (220 kDa). The rod domain contains 11 cryptic VBS (drawn in blue). The dimerization domain is a single helix that sits at the end of the rod domain. B. (left) In the initial stage of FA formation, the talin dimer binds to actin and integrin. At this stage, the cryptic VBSs remain buried among the α-helical bundles. (right) As the actin filament starts to pull on talin, the formerly buried VBS are revealed to allow vinculin binding, and cause more actin filament recruitment.

  • How to switch the motor on: RNA polymerase initiation steps at the single-molecule level

    How to switch the motor on: RNA polymerase initiation steps at the single‐molecule level

    Transcription initiation scheme: This review focuses on the initiation process and how its intermediates have been recently unraveled by single-molecule techniques. RNAP initiation is divided into three substeps that correspond to the three subsections of this review: I: the promoter search process (green background), II: the transition from the closed complex to the open complex (red background), and III: the mechanisms of initial transcription and promoter escape (yellow background). Based on ref 11.

  • The chaperone toolbox at the single-molecule level: From clamping to confining

    The chaperone toolbox at the single‐molecule level: From clamping to confining

    Interactions between trigger factor and client proteins. (A) Interaction sites on TF for MBP as derived from NMR experiments. (B) Interaction of TF with a partial fold of MBP, as determined by MD simulations, and observed by optical tweezers experiments (panels c–e). (C) Single-molecule optical tweezers experimental setup with MBP tethered between two polystyrene beads. One bead is held on a pipette, while the other is held by an optical trap that is also used to determine the applied force. Pulling experiments on MBP in isolation (D) and MBP with TF present (E) show an increased presence of partially folded states for the latter, during pulling and also during refolding at low force in between pulling cycles. Panel A is redrawn from Saio et al., panel B from Singhal et al., panels C–E from Mashaghi et al.

  • Studying transcription initiation by RNA polymerase with diffusion-based single-molecule fluorescence

    Studying transcription initiation by RNA polymerase with diffusion‐based single‐molecule fluorescence

    High-resolution structure of Thermus aquaticus core RNAP (PDB 1HQM). Figure generated using PyMol. (A) The five RNAP subunits are represented with different colors: The two α subunits are blue, β′ is grey, β is orange, and ω is magenta. Two orientations (related by ∼180° rotation) are shown, with the LEFT showing the trailing edge of RNAP facing upstream DNA and the RIGHT showing the leading edge facing downstream DNA. The cleft between the β′ clamp and β lobes (the pincers) forms the primary channel, while the secondary channel is arranged on the opposite face of RNAP. (B) The catalytic magnesium (cyan sphere), bridge helix (red), trigger loop (green), and F-loop (yellow) of the active site can be seen from the downstream facing side of RNAP.

  • Proteins mediating DNA loops effectively block transcription
  • Single‐molecule imaging reveals the translocation and DNA looping dynamics of hepatitis C virus NS3 helicase
  • Molecular stretching modulates mechanosensing pathways
  • How to switch the motor on: RNA polymerase initiation steps at the single‐molecule level
  • The chaperone toolbox at the single‐molecule level: From clamping to confining
  • Studying transcription initiation by RNA polymerase with diffusion‐based single‐molecule fluorescence

Recently Published Issues

See all

Recently Published Articles

Interactive Figures

Learn More

PROTEINS Imolecules












Author Shigeki Arai on his recently published Protein Science paper entitled " An insight into the thermodynamic characteristics of human thrombopoietin complexation with TN1 antibody." Read the paper here

Watch More Videos

Protein Science

Protein Science

PRO VI Canada

Cryo-Electron Microscopy

Protein Science Awards

2017 Best Paper Award

2017 Best Paper Award Winners
We are pleased to announce the winners of the 2017 Protein Science Best Paper Award:

Charlotte Miton
Postdoctoral Research Fellow
Michael Smith Laboratories at University of British Columbia

How mutational epistasis impairs predictability in protein evolution and design
Charlotte M. Miton and Nobuhiko Tokuriki
Protein Sci. 25:1260-1272, 2016.

Zach Schaefer
Graduate Student
Department of Biochemistry and Molecular Biology at University of Chicago

A polar ring endows improved specificity to an antibody fragment
Zachary P. Schaefer, Lucas J. Bailey and Anthony A. Kossiakoff
Protein Sci. 25:1290-1298, 2016.

_________________________

2017 Young Investigator Award Winner

The Protein Science Young Investigator Award recognizes a scientist generally within the first 8 years of an independent career who has made an important contribution to the study of proteins. The 2017 winner is Dr. David Pagliarini (University of Wisconsin, Madison).

_________________________

More information on our awards can be found here.

Get access to the latest research anywhere, anytime

Download the journal app to your Apple and Android Devices Now!

Download the journal app now!

Download the journal app now!

SEARCH

SEARCH BY CITATION