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Special Issue "NMR as a Tool to Investigate Biomolecular Structure, Recognition and Dynamics"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: 10 July 2018

Special Issue Editor

Guest Editor
Prof. Brian F. Volkman

Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
Website | E-Mail
Phone: 414-955-8400
Interests: protein structure; NMR spectroscopy; chemokine; GPCR; protein dynamics; fragment-based drug discovery; biased agonism

Special Issue Information

Dear Colleagues,

The emergent properties of living systems derive from the assembly and fluctuation of biomolecules—proteins, nucleic acids, lipids, carbohydrates—in an aqueous environment. For over 50 years, nuclear magnetic resonance (NMR) spectroscopy has been an indispensable tool in biology and its importance in translational research and clinical medicine is growing rapidly. Continual advances in isotopic labeling, instrument performance, and multidimensional NMR methods expand its range of accessibility to molecular systems of ever-increasing size and complexity, including intact cells and tissues. Solution and solid-state NMR are routinely used to solve 3D structures of biomolecular complexes, monitor ligand binding and other types of molecular recognition events, and measure molecular motions across a vast range of timescales. Chemical shifts, coupling constants, relaxation times and other NMR parameters can be combined with data from other biophysical methods and computational modeling to develop realistic descriptions of flexible molecular systems. Translational and clinical applications of NMR include chemical ligand screening for drug discovery, metabolomic analysis of plasma, urine, and cerebrospinal fluid, and FDA-approved diagnostic testing of blood lipoprotein levels. This Special Issue of Molecules illustrates the broad impact on biology and medicine of NMR spectroscopy as a tool to investigate biomolecular structure, recognition and dynamics.

Prof. Dr. Brian F. Volkman
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 papers will be 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. Molecules 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 1800 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.


  • nuclear magnetic resonance
  • protein
  • DNA
  • RNA
  • carbohydrate
  • lipid
  • relaxation
  • chemical shift
  • stable isotope
  • triple-resonance
  • non-uniform sampling
  • fragment-based screening
  • metabolomics

Published Papers (1 paper)

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Open AccessArticle Substrate Binding Switches the Conformation at the Lynchpin Site in the Substrate-Binding Domain of Human Hsp70 to Enable Allosteric Interdomain Communication
Molecules 2018, 23(3), 528; doi:10.3390/molecules23030528
Received: 4 February 2018 / Revised: 18 February 2018 / Accepted: 24 February 2018 / Published: 27 February 2018
PDF Full-text (3568 KB) | HTML Full-text | XML Full-text | Supplementary Files
The stress-induced 70 kDa heat shock protein (Hsp70) functions as a molecular chaperone to maintain protein homeostasis. Hsp70 contains an N-terminal ATPase domain (NBD) and a C-terminal substrate-binding domain (SBD). The SBD is divided into the β subdomain containing the substrate-binding site (βSBD)
[...] Read more.
The stress-induced 70 kDa heat shock protein (Hsp70) functions as a molecular chaperone to maintain protein homeostasis. Hsp70 contains an N-terminal ATPase domain (NBD) and a C-terminal substrate-binding domain (SBD). The SBD is divided into the β subdomain containing the substrate-binding site (βSBD) and the α-helical subdomain (αLid) that covers the βSBD. In this report, the solution structures of two different forms of the SBD from human Hsp70 were solved. One structure shows the αLid bound to the substrate-binding site intramolecularly, whereas this intramolecular binding mode is absent in the other structure solved. Structural comparison of the two SBDs from Hsp70 revealed that client-peptide binding rearranges residues at the interdomain contact site, which impairs interdomain contact between the SBD and the NBD. Peptide binding also disrupted the inter-subdomain interaction connecting the αLid to the βSBD, which allows the binding of the αLid to the NBD. The results provide a mechanism for interdomain communication upon substrate binding from the SBD to the NBD via the lynchpin site in the βSBD of human Hsp70. In comparison to the bacterial ortholog, DnaK, some remarkable differences in the allosteric signal propagation among residues within the Hsp70 SBD exist. Full article

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Studying Glycosaminoglycan-Protein Interactions Using NMR Spectroscopy
Authors: Vitor H. Pomin 1 and Xu Wang 2
Affiliation: 1. Department of Biomolecular Sciences, and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi. (vpomin@olemiss.edu)
2. School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA (xu.wang.4@asu.edu).
Abstract: The formation of intermolecular complexes between glycosaminoglycans (GAGs) and functional proteins is a crucial event in numerous pathophysiological systems. Nuclear Magnetic Resonance (NMR) is one of the most utilized and informative analytical techniques for investigating GAG-protein complexes. Although current NMR techniques such as chemical shift perturbation, saturation transfer difference and transferred nuclear Overhauser effect have revealed valuable information on protein-GAG systems, elucidating high-resolution structures of GAG-protein complexes and studying the dynamics of these often transient interactions continue to be challenging. In addition, obtaining structurally homogeneous and isotopically enriched GAG ligands for structural investigations is also difficult. As a result, understanding of the structure-activity relationship involving GAGs is still primitive. To overcome these deficiencies, several innovative NMR techniques have been developed recently. Here we review some of the latest NMR studies of the physicochemical and biological properties of the various GAG-protein complexes with an emphasize on summarizing the development and utilization of novel NMR techniques that can shed new insights into structure and dynamics of GAG-protein interactions. In particular, we will discuss methods to produce isotopically enriched as well as paramagnetically tagged GAG ligands and novel approaches focused on examining lysine and arginine side chains to identify GAG-binding sites in binding proteins. Results obtained from solid-state NMR will be also presented. Finally, we will discuss the nature of GAG-protein interactions revealed by these studies and their contributions to the understanding of structure-activity relationship of GAGs.

Authors: Fariba Assadi-Porter *, James Radek, Hongyu Rao and Marco Tonelli
Affiliation: Department of Integrative Biology, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
Email: fariba@nmrfam.wisc.edu
Abstract: Taste signaling is a complex process that is linked to obesity and its associated metabolic syndromes. The sweet taste is mediated through a heterodimeric G protein coupled receptor (GPCR) in a species-specific manner and at multi-tissue specific levels. The sweet receptor recognizes a large number of ligands with structural and functional diversities to modulate different amplitudes of downstream signaling pathway(s). The human sweet-taste receptor has been extremely difficult to study by biophysical methods due to inadequate methods for producing large homogeneous quantities of the taste-receptor protein and a lack of reliable in vitro assays to precisely measure productive ligand binding modes leading to activity upon their interactions with the receptor protein. We report a multimodal high throughput assays to monitor ligand binding, receptor stability and conformational changes to model the molecular interactions between ligand-receptor. We applied saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR) complemented by differential scanning calorimetry (DSC), circular dichroism (CD) spectroscopy and molecular docking simulations to characterize and dissect binding interactions. Our method using complementary NMR-STD and biophysical analysis is advantageous to study the mechanism of ligand binding and signaling processes in other GPCRs.

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