Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

Conformational Studies of Proteins and Peptides

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Benefits of Publishing in a Special Issue
Published Papers

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

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 6599

Share This Special Issue

Special Issue Editors

Prof. Dr. Mahmoud Ghomi

E-Mail Website
Guest Editor

Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain
Interests: molecular biophysics; optical spectroscopy; biomolecular structure and dynamics
Special Issues, Collections and Topics in MDPI journals

Dr. Santiago Sanchez-Cortés

E-Mail Website
Guest Editor

Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain
Interests: plasmonic nanoparticles; surface enhanced Raman scattering; optical spectroscopy
Special Issues, Collections and Topics in MDPI journals

Dr. Belén Hernández

E-Mail Website
Guest Editor

LVTS, INSERM U1148, Université Sorbonne Paris Nord, 74 rue Marcel Cachin, 93017 Bobigny Cédex, France
Interests: biophysics; peptide structure; protein structure; optical spectroscopies; Raman scattering; FT-IR absorption

Special Issue Information

Dear Colleagues,

Proteins and linear heteropolymers, the backbone of which is formed by successive peptide bonds between natural amino acids, provide a wealth of structural properties. Despite the fact that the conformational flexibility of each polymer residue is simply governed by three torsion angles (f, y, w), a variety of forms is expected in relation to the values assigned to these angles (helices, sheets, and turns, etc.). With structure and function being closely related in proteins, the global conformation adopted by a peptide chain determines its function. The surrounding water molecules and their dynamics also play a pivotal role in the chain folding of globular proteins, in maintaining the disordered character of chains, and in inducing their aggregation processes, which are known as the main cause of several human diseases such as Alzheimer’s, Parkinson’s and type‑II diabetes. Short size peptide chains are recognized as efficient bioactive, functional and imaging agents. Their versatility for elaborating therapeutic agents, used, for instance, as analogues of natural hormones, as well for as innovating synthetic materials has been emphasized over the past two decades. In this Special Issue, our aim is to explore the capability of different physical techniques such as X-ray diffraction/scattering, NMR, optical spectroscopies (electronic circular dichroism, FT-IR absorption, vibrational circular dichroism, Raman scattering, Raman optical activity), in combination with adequate theoretical methods, to elucidate the structural features of proteins and peptides.

Prof. Dr. Mahmoud Ghomi
Dr. Santiago Sanchez-Cortés
Dr. Belén Hernández
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. 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.

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

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

Published Papers (4 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

19 pages, 2921 KiB

Open AccessArticle

Influence of Side Chain–Backbone Interactions and Explicit Hydration on Characteristic Aromatic Raman Fingerprints as Analysed in Tripeptides Gly-Xxx-Gly (Xxx = Phe, Tyr, Trp)

by Belén Hernández, Yves-Marie Coïc, Sergei G. Kruglik, Santiago Sanchez-Cortes and Mahmoud Ghomi

Int. J. Mol. Sci. 2025, 26(8), 3911; https://doi.org/10.3390/ijms26083911 - 21 Apr 2025

Viewed by 573

Abstract

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800–600 cm⁻¹) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (F_i = 1, …, 6) in Phe, (Y_i = 1, …, 7) in Tyr, and (W_i = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5–7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850–830 cm⁻¹) and Trp (~1360–1340 cm⁻¹), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds. Full article

(This article belongs to the Special Issue Conformational Studies of Proteins and Peptides)

► Show Figures

Graphical abstract

14 pages, 2462 KiB

Open AccessArticle

The Use of Dansyl Chloride to Probe Protein Structure and Dynamics

by James Larson, Monika Tokmina-Lukaszewska, Jadyn Malone, Ethan J. Hasenoehrl, Will Kelly, Xuelan Fang, Aidan White, Angela Patterson and Brian Bothner

Int. J. Mol. Sci. 2025, 26(2), 456; https://doi.org/10.3390/ijms26020456 - 8 Jan 2025

Viewed by 1139

Abstract

Dansyl labeling is a widely used approach for enhancing the detection of small molecules by UV spectroscopy and mass spectrometry. It has been successfully applied to identify and quantify a variety of biological and environmental specimens. Despite clear advantages, the dansylation reaction has found very few applications in the study of proteins. We reasoned that the mild labeling conditions, small size, and rapid reaction could be beneficial for studying protein structure and dynamics. To test this, we investigated the impact of dansylation on protein fold, stability, protein–protein, and protein–cofactor interactions. We selected two model proteins, myoglobin and alcohol dehydrogenase, for analysis using native mass spectrometry and ion mobility mass spectrometry. Our work establishes the utility of dansyl chloride as a covalent probe to study protein structure and dynamics under native conditions. Full article

(This article belongs to the Special Issue Conformational Studies of Proteins and Peptides)

► Show Figures

Figure 1

23 pages, 5245 KiB

Open AccessArticle

Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy

by Holly Freedman and Jack A. Tuszynski

Int. J. Mol. Sci. 2024, 25(12), 6406; https://doi.org/10.3390/ijms25126406 - 10 Jun 2024

Cited by 1 | Viewed by 2303

Abstract

The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin’s chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin. Full article

(This article belongs to the Special Issue Conformational Studies of Proteins and Peptides)

► Show Figures

Graphical abstract

12 pages, 1366 KiB

Open AccessArticle

Steady-State and Time-Resolved Fluorescence Study of Selected Tryptophan-Containing Peptides in an AOT Reverse Micelle Environment

by Krystian Gałęcki, Agnieszka Kowalska-Baron, Katarzyna E. Nowak, Anna Gajda and Beata Kolesińska

Int. J. Mol. Sci. 2023, 24(20), 15438; https://doi.org/10.3390/ijms242015438 - 22 Oct 2023

Cited by 2 | Viewed by 1879

Abstract

The aim of this study was to demonstrate the utility of time-resolved fluorescence spectroscopy in the detection of subtle changes in the local microenvironment of a tryptophan chromophore in a confined and crowded medium of AOT reverse micelles, which mimic biological membranes and cell compartmentalization. For this purpose, fluorescence properties of L-tryptophan and several newly synthesized tryptophan-containing peptides in buffer and in an AOT reverse micelle medium were determined. It was shown that insertion of tryptophan and its short di- and tripeptides inside micelles led to evident changes in both the steady-state emission spectra and in fluorescence decay kinetics. The observed differences in spectral characteristics, such as a blue shift in the emission maxima, changes in the average fluorescence lifetime, and the appearance of environmental-dependent fluorescent species, showed the utility of time-resolved fluorescence spectroscopy as a sensitive tool for detecting subtle conformational modifications in tryptophan and its peptides induced by changes in polarity, viscosity, and specific interactions between chromophores and water molecules/polar groups/ions that occur inside reverse micelles. Full article

(This article belongs to the Special Issue Conformational Studies of Proteins and Peptides)

► Show Figures

Journal Menu

Journal Browser

Conformational Studies of Proteins and Peptides

Share This Special Issue

Special Issue Editors

Special Issue Information

Benefits of Publishing in a Special Issue

Published Papers (4 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI