Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.1
4.9
Journals
IJMS
Special Issues
Probing Protein Conformational Plasticity
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Probing Protein Conformational Plasticity

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 3660

Special Issue Editor

Dr. Andreas Stadler

E-Mail Website
Guest Editor
1. Forschungszentrum Jülich, IBI-8/JCNS-1, 52428 Jülich, Germany
2. Institut für Physikalische Chemie, RWTH Aachen University, 52074 Aachen, Germany
Interests: neutron scattering; protein dynamics; small-angle scattering; X-ray scattering

Special Issue Information

Dear Colleagues,

It has been becoming clear in the recent years that regulation of conformational plasticity of proteins plays a pivotal role for various biological functions on the molecular level.

Intrinsically disordered and partially folded proteins are prime examples for flexible biomacromolecules that sample a broad conformational space and exhibit polymer-like properties. Regulation of protein dynamics and conformational plasticity plays a key role for a range of biologically relevant phenomena such as, for instance, protein thermal stability, protein-ligand interactions, and enzymatic catalysis. Protein flexibility is crucially important for the subtle interplay of proteins with their hydration layer and affects macromolecular diffusion.

Recently, a wide range of state-of-the art experimental techniques and computer simulation methods have emerged that are used to probe the relevance of protein conformational plasticity for protein function on multiple time and length scales.

In this Special Issue of IJMS, we want to offer a platform for high-quality publications on experimental and simulation studies that address that research field.

Dr. Andreas Stadler
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • flexible and disordered proteins
  • protein stability and dynamics
  • modulation of conformational dynamics by ligand binding
  • protein dynamics in enzymatic catalysis
  • protein - hydration layer interactions
  • protein diffusion
  • neutron
  • X-ray
  • light scattering techniques
  • NMR spectroscopy
  • single-molecule spectroscopy
  • computer simulations

Published Papers (2 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

15 pages, 706 KiB  
Article
Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems
by Shilpa Mohanakumar, Namkyu Lee and Simone Wiegand
Int. J. Mol. Sci. 2022, 23(22), 14198; https://doi.org/10.3390/ijms232214198 - 17 Nov 2022
Cited by 3 | Viewed by 1502
Abstract
In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying microscopic physical effect is still not understood, but often attributed to changes in the hydration layer once the binding occurs. To gain deeper insight, we investigate whether [...] Read more.
In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying microscopic physical effect is still not understood, but often attributed to changes in the hydration layer once the binding occurs. To gain deeper insight, we investigate whether non-equilibrium coefficients can be related to equilibrium properties. Therefore, we compare thermophoretic data measured by thermal diffusion forced Rayleigh scattering (TDFRS) (which is a non-equilibrium process) with thermodynamic data obtained by isothermal titration calorimetry (ITC) (which is an equilibrium process). As a reference system, we studied the chelation reaction between ethylenediaminetetraacetic acid (EDTA) and calcium chloride (CaCl2) to relate the thermophoretic behavior quantified by the Soret coefficient ST to the Gibb’s free energy ΔG determined in the ITC experiment using an expression proposed by Eastman. Finally, we have studied the binding of the protein Bovine Carbonic Anhydrase I (BCA I) to two different benzenesulfonamide derivatives: 4-fluorobenzenesulfonamide (4FBS) and pentafluorobenzenesulfonamide (PFBS). For all three systems, we find that the Gibb’s free energies calculated from ST agree with ΔG from the ITC experiment. In addition, we also investigate the influence of fluorescent labeling, which allows measurements in a thermophoretic microfluidic cell. Re-examination of the fluorescently labeled system using ITC showed a strong influence of the dye on the binding behavior. Full article
(This article belongs to the Special Issue Probing Protein Conformational Plasticity)
►▼ Show Figures

Graphical abstract

19 pages, 2620 KiB  
Article
Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride
by Luman Haris, Ralf Biehl, Martin Dulle, Aurel Radulescu, Olaf Holderer, Ingo Hoffmann and Andreas M. Stadler
Int. J. Mol. Sci. 2022, 23(13), 6969; https://doi.org/10.3390/ijms23136969 - 23 Jun 2022
Cited by 3 | Viewed by 1484
Abstract
Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin–echo spectroscopy (NSE). [...] Read more.
Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin–echo spectroscopy (NSE). A concentration of 0.2 M GndCl causes charge screening in MBP resulting in a compact, but still disordered protein conformation, while GndCl concentrations above 1 M lead to structural expansion and swelling of MBP. NSE data of MBP were analyzed using the Zimm model with internal friction (ZIF) and normal mode (NM) analysis. A significant contribution of internal friction was found in compact states of MBP that approaches a non-vanishing internal friction relaxation time of approximately 40 ns at high GndCl concentrations. NM analysis demonstrates that the relaxation rates of internal modes of MBP remain unaffected by GndCl, while structural expansion due to GndCl results in increased amplitudes of internal motions. Within the model of the Brownian oscillator our observations can be rationalized by a loss of friction within the protein due to structural expansion. Our study highlights the intimate coupling of structural and dynamical plasticity of MBP, and its fundamental difference to the behavior of ideal polymers in solution. Full article
(This article belongs to the Special Issue Probing Protein Conformational Plasticity)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-2
Back to TopTop