Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
8.3
5.5
Journals
Biomolecules
Special Issues
Macromolecular Folding and Dynamics
share announcement

Macromolecular Folding and Dynamics

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 6179

Special Issue Editors

Dr. Gang (Gary) Ren

E-Mail Website
Guest Editor
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Interests: single-molecule 3D structure, cryo-electron tomography, macromolecular dynamics and folding
Dr. Corie Ralston

E-Mail Website
Guest Editor
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
Interests: X-ray; structural characterization
Dr. Rohit Jain

E-Mail Website
Guest Editor
School of Medicine, Case Western Reserve University, Cleveland, OH, USA
Interests: structural biology; protein folding; mass spectrometry; biosensors; protein footprinting

Special Issue Information

Dear Colleagues,

The goal of this Special Issue is to highlight some recent advances in characterization of macromolecular structural dynamics and folding. We focus here on new and existing tools to analyze conformational organization, including single-molecule 3D structure determination and location, characterization of macromolecular dynamics and folding/unfolding, the dynamics of structural transitions, and methods for probing rapid and small motions of macromolecules in solution. Through elucidation of intermediate conformations and dynamics, the landscape of structure and energy can enable us to understand the comprehensive spatial and kinetic organization of macromolecules in living cells.

Dr. Gang (Gary) Ren
Dr. Corie Ralston
Dr. Rohit Jain
Guest Editors

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. Biomolecules 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 2700 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

  • macromolecular dynamics
  • macromolecular folding
  • structural characterization
  • structural heterogeneity
  • structural transitions

Published Papers (3 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

Jump to: Review

11 pages, 1997 KiB  
Article
Features of Protein Unfolding Transitions and Their Relation to Domain Topology Probed by Single-Molecule FRET
by Nuno Bustorff and Jörg Fitter
Biomolecules 2023, 13(9), 1280; https://doi.org/10.3390/biom13091280 - 22 Aug 2023
Viewed by 922
Abstract
A protein fold is defined as a structural arrangement of a secondary structure in a three-dimensional space. It would be interesting to know whether a particular fold can be assigned to certain features of the corresponding folding/unfolding transitions. To understand the underlying principles [...] Read more.
A protein fold is defined as a structural arrangement of a secondary structure in a three-dimensional space. It would be interesting to know whether a particular fold can be assigned to certain features of the corresponding folding/unfolding transitions. To understand the underlying principles of the manifold folding transitions in more detail, single-molecule FRET is the method of choice. Taking the two-domain protein phosphoglycerate kinase (PGK) as an example, we investigated denaturant-induced unfolded states of PGK using the above method. For this purpose, different intramolecular distances within the two domains were measured. In addition to the known two-state transition, a transition with a compact folding intermediate was also identified in each of the two domains. Based on the structural homology of the domains (characterized by a Rossmann fold) and the striking similarity in the features of the measured distance changes during unfolding, clear evidence emerged that the underlying domain topology plays an important role in determining the observed structural changes. Full article
(This article belongs to the Special Issue Macromolecular Folding and Dynamics)
►▼ Show Figures

Figure 1

17 pages, 6891 KiB  
Article
Isolation and Characterization of the Arapaima gigas Growth Hormone (ag-GH) cDNA and Three-Dimensional Modeling of This Hormone in Comparison with the Human Hormone (hGH)
by Eliana Rosa Lima, Renan Passos Freire, Miriam Fussae Suzuki, João Ezequiel Oliveira, Vanessa Luna Yosidaki, Cibele Nunes Peroni, Thaís Sevilhano, Moisés Zorzeto, Lucas Simon Torati, Carlos Roberto Jorge Soares, Igor Daniel de Miranda Lima, Thales Kronenberger, Vinicius Gonçalves Maltarollo and Paolo Bartolini
Biomolecules 2023, 13(1), 158; https://doi.org/10.3390/biom13010158 - 12 Jan 2023
Viewed by 2232
Abstract
In a previous work, the common gonadotrophic hormone α-subunit (ag-GTHα), the ag-FSH β- and ag-LH β-subunit cDNAs, were isolated and characterized by our research group from A. gigas pituitaries, while a preliminary synthesis of ag-FSH was also carried out in human embryonic kidney [...] Read more.
In a previous work, the common gonadotrophic hormone α-subunit (ag-GTHα), the ag-FSH β- and ag-LH β-subunit cDNAs, were isolated and characterized by our research group from A. gigas pituitaries, while a preliminary synthesis of ag-FSH was also carried out in human embryonic kidney 293 (HEK293) cells. In the present work, the cDNA sequence encoding the ag-growth hormone (ag-GH) has also been isolated from the same giant Arapaimidae Amazonian fish. The ag-GH consists of 208 amino acids with a putative 23 amino acid signal peptide and a 185 amino acid mature peptide. The highest identity, based on the amino acid sequences, was found with the Elopiformes (82.0%), followed by Anguilliformes (79.7%) and Acipenseriformes (74.5%). The identity with the corresponding human GH (hGH) amino acid sequence is remarkable (44.8%), and the two disulfide bonds present in both sequences were perfectly conserved. Three-dimensional (3D) models of ag-GH, in comparison with hGH, were generated using the threading modeling method followed by molecular dynamics. Our simulations suggest that the two proteins have similar structural properties without major conformational changes under the simulated conditions, even though they are separated from each other by a >100 Myr evolutionary period (1 Myr = 1 million years). The sequence found will be used for the biotechnological synthesis of ag-GH while the ag-GH cDNA obtained will be utilized for preliminary Gene Therapy studies. Full article
(This article belongs to the Special Issue Macromolecular Folding and Dynamics)
►▼ Show Figures

Figure 1

Review

Jump to: Research

27 pages, 1171 KiB  
Review
Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery
by Shuqi Luo, Samuel Wohl, Wenwei Zheng and Sichun Yang
Biomolecules 2023, 13(3), 530; https://doi.org/10.3390/biom13030530 - 14 Mar 2023
Cited by 1 | Viewed by 2459
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and [...] Read more.
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors. Full article
(This article belongs to the Special Issue Macromolecular Folding and Dynamics)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop