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Symmetry
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Symmetry in Structural Biology
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Symmetry in Structural Biology

A special issue of Symmetry (ISSN 2073-8994).

Deadline for manuscript submissions: closed (15 August 2017) | Viewed by 20154

Special Issue Editor

Dr. John Vakonakis

E-Mail Website
Guest Editor
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
Interests: macromolecular interactions and assemblies; structural biology; X-ray crystallography; NMR

Special Issue Information

Dear Colleagues,

For many of us, fascination with structural biology was triggered by the promise of describing biological macromolecules as microscopic machines. Others were attracted by the potential for understanding cellular function at the atomic level, or the undeniable beauty of proteins and nucleic acids when viewed in 3D space. Whether seeking to resolve mechanisms or for aesthetic reasons, we all appreciate that the symmetry inherent in many biological systems is a key parameter of our investigations. This Special Issue intends to celebrate symmetry in structural biology by bringing together selected papers on the many ways this phenomenon contributes in molecular and cellular mechanisms, and in our investigations of these systems. Themes for submission may include (but are not limited to):

Symmetry in biological macromolecules

  • Symmetric molecules
  • Repetitive units
  • Pseudo-symmetry
  • Symmetry in molecular function

Symmetry in macromolecular assemblies

  • Homo- and hetero-oligomers
  • Symmetry at the sub-cellular level
  • Symmetry in viruses

Symmetry in structural methods

  • Crystallography
  • Symmetry in data handling
  • Symmetry in structural restraints

Prof. John Vakonakis
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Symmetry is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Protein and nucleic acid structures
  • Macromolecular assemblies
  • Repetitive units
  • Symmetry versus pseudo-symmetry
  • Molecular and cellular function
  • Structural biology methods

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

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9819 KiB  
Article
Symmetry and Structure in the POT Family of Proton Coupled Peptide Transporters
by Simon Newstead
Symmetry 2017, 9(6), 85; https://doi.org/10.3390/sym9060085 - 14 Jun 2017
Cited by 2 | Viewed by 6930
Abstract
The POT family of proton coupled oligopeptide transporters belong to the Major Facilitator Superfamily of secondary active transporters and are found widely distributed in bacterial, plant, fungal and animal genomes. POT transporters use the inwardly directed proton electrochemical gradient to drive the concentrative [...] Read more.
The POT family of proton coupled oligopeptide transporters belong to the Major Facilitator Superfamily of secondary active transporters and are found widely distributed in bacterial, plant, fungal and animal genomes. POT transporters use the inwardly directed proton electrochemical gradient to drive the concentrative uptake of di- and tri-peptides across the cell membrane for metabolic assimilation. Mammalian members of the family, PepT1 and PepT2, are responsible for the uptake and retention of dietary protein in the human body, and due to their promiscuity in ligand recognition, play important roles in the pharmacokinetics of drug transport. Recent crystal structures of bacterial and plant members have revealed the overall architecture for this protein family and provided a framework for understanding proton coupled transport within the POT family. An interesting outcome from these studies has been the discovery of symmetrically equivalent structural and functional sites. This review will highlight both the symmetry and asymmetry in structure and function within the POT family and discuss the implications of these considerations in understanding transport and regulation. Full article
(This article belongs to the Special Issue Symmetry in Structural Biology)
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378 KiB  
Article
On the Charge Density Refinement of Odd-Order Multipoles Invariant under Crystal Point Group Symmetry
by Pietro Roversi and Riccardo Destro
Symmetry 2017, 9(5), 63; https://doi.org/10.3390/sym9050063 - 26 Apr 2017
Cited by 1 | Viewed by 3803
Abstract
Charge density studies utilise a multipolar expansion of the atomic density (and the associated atomic scattering factor) in order to model asphericity. Contributions of the individual multipoles to the atomic density are then refined as multipole population coefficients. Refinement of these coefficients pertaining [...] Read more.
Charge density studies utilise a multipolar expansion of the atomic density (and the associated atomic scattering factor) in order to model asphericity. Contributions of the individual multipoles to the atomic density are then refined as multipole population coefficients. Refinement of these coefficients pertaining to odd-order multipoles that are invariant under the crystal point-group symmetry is often problematic, with ill-defined values and correlations plaguing the convergence to a good model. These difficulties have been discussed in generic terms in the literature, but never explicitly analysed in detail. In this communication, we show that the charge density multipolar atomic scattering factor can be partitioned in three contributions that differ in their behaviour under the point group symmetry of the crystal. This partitioning rationalises and predicts the conditions that give rise to ill-conditioning of the charge density refinement of these multipoles. Full article
(This article belongs to the Special Issue Symmetry in Structural Biology)
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Review

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3222 KiB  
Review
Coupling Form and Function: How the Oligomerisation Symmetry of the SAS-6 Protein Contributes to the Architecture of Centriole Organelles
by Jodie E. Ford, Phillip J. Stansfeld and Ioannis Vakonakis
Symmetry 2017, 9(5), 74; https://doi.org/10.3390/sym9050074 - 16 May 2017
Viewed by 4646
Abstract
Centrioles make up the centrosome and basal bodies in animals and as such play important roles in cell division, signalling and motility. They possess characteristic 9-fold radial symmetry strongly influenced by the protein SAS-6. SAS-6 is essential for canonical centriole assembly as it [...] Read more.
Centrioles make up the centrosome and basal bodies in animals and as such play important roles in cell division, signalling and motility. They possess characteristic 9-fold radial symmetry strongly influenced by the protein SAS-6. SAS-6 is essential for canonical centriole assembly as it forms the central core of the organelle, which is then surrounded by microtubules. SAS-6 self-assembles into an oligomer with elongated spokes that emanate towards the outer microtubule wall; in this manner, the symmetry of the SAS-6 oligomer influences centriole architecture and symmetry. Here, we summarise the form and symmetry of SAS-6 oligomers inferred from crystal structures and directly observed in vitro. We discuss how the strict 9-fold symmetry of centrioles may emerge, and how different forms of SAS-6 oligomers may be accommodated in the organelle architecture. Full article
(This article belongs to the Special Issue Symmetry in Structural Biology)
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Other

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872 KiB  
Letter
Gate Antiphase of Potassium Channel
by Yuval Ben-Abu
Symmetry 2017, 9(8), 150; https://doi.org/10.3390/sym9080150 - 8 Aug 2017
Cited by 4 | Viewed by 3990
Abstract
Potassium channels are integral membrane proteins that selectively transport K+ ions across cell membranes. They function through a pair of gates, which work in tandem to allow the passage of the ions through the channel pore in a coupled system, to which [...] Read more.
Potassium channels are integral membrane proteins that selectively transport K+ ions across cell membranes. They function through a pair of gates, which work in tandem to allow the passage of the ions through the channel pore in a coupled system, to which I refer to here as the “gate linker”. The functional mutation effects, as described in the literature, suggest that the gate linker functions analogously to a triad of coiled springs arranged in series. Accordingly, I constructed a physical model of harmonic oscillators and analyzed it mechanically and mathematically. The operation of this model indeed corresponds to the phenomena observed in the mutations study. The harmonic oscillator model shows that the strength of the gate linker is crucial for gate coupling and may account for the velocity, direction, and efficiency of ion transfer through the channel. Such a physical perspective of the gating process suggests new lines of investigation regarding the coupling mode of potassium channels and may help to explain the importance of the gate linker to channel function. Full article
(This article belongs to the Special Issue Symmetry in Structural Biology)
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