Article
Biochemistry & Molecular Biology
Livia Pagano, Valeria Pennacchietti, Awa Diop, Daniele Santorelli, Paola Pietrangeli, Lucia Marcocci, Caterina Nardella, Francesca Malagrino, Angelo Toto, Stefano Gianni
Summary: In this study, the folding properties of the multidomain protein Grb2 were analyzed, revealing the interaction between the SH2 and C-SH3 domains during folding. These findings contribute to a better understanding of multidomain protein folding.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Leonore Novak, Maria Petrosino, Daniele Santorelli, Roberta Chiaraluce, Valerio Consalvi, Alessandra Pasquo, Carlo Travaglini-Allocatelli
Summary: A Phi value analysis was conducted on BRD2(2) to investigate its folding pathway, revealing that the C-terminal region serves as the initial folding nucleus, with the N-terminal region consolidating its structure later in the process. This indicates a hierarchical mechanism of protein folding with non-native interactions playing a significant role.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Daisuke Fujinami, Seiichiro Hayashi, Daisuke Kohda
Summary: The study characterized the transition state of a two-state slow topological isomerization of a lantibiotic peptide using exchange spectroscopy. The exchange kinetic rates varied per residue and showed a linear relationship with the logarithm of the equilibrium constants.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biochemistry & Molecular Biology
George D. Rose
Summary: The article introduces a mechanism in protein folding that emphasizes conformational entropy as the main organizer, suggesting that hydrogen bond satisfaction is thermodynamically necessary. It points out that the satisfaction or dissatisfaction of hydrogen bonds has a significant impact on the stability of proteins.
Article
Biochemistry & Molecular Biology
Rupam Bhattacharjee, Jayant B. Udgaonkar
Summary: The unfolding mechanism of a small heterodimeric protein has been characterized using hydrogen exchange-mass spectrometry, revealing a five-state mechanism for transient structure opening. Structural changes occur gradually in the first three steps, and cooperatively in the last step.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Simone Carrino, Christopher D. Hennecker, Ana C. Murrieta, Anthony Mittermaier
Summary: Human chromosomes have long, single-stranded DNA overhangs with repetitive sequences (TTAGGG)n at the termini, which can fold into guanine quadruplexes (GQ). The folding of GQs within these chains is influenced by folding frustration and negative cooperativity, leading to increased unfolding of TTAGGG repeats and potential binding sites for telomeric proteins. This phenomenon is particularly pronounced at the chain termini, suggesting a role in telomere extension by telomerase.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Valeria Jaramillo-Martinez, Matthew J. Dominguez, Gemma M. Bell, Megan E. Souness, Anna H. Carhart, M. Adriana Cuibus, Elahe Masoumzadeh, Benjamin J. Lantz, Aaron J. Adkins, Michael P. Latham, K. Aurelia Ball, Elliott J. Stollar
Summary: Charged residues on protein surfaces play important roles in protein stability and interactions. Proteins with highly charged binding regions have weak stability due to electrostatic repulsion, but these regions are useful for binding to oppositely charged targets. Increasing salt concentration stabilizes the protein folds by mimicking electrostatic interactions during target binding. The yeast SH3 domain was studied to understand the contributions of electrostatic and hydrophobic interactions in folding. The addition of salt primarily affects the folding rate, indicating that hydrophobic collapse and electrostatic repulsion occur in the transition state.
Article
Chemistry, Physical
Angelina Folberth, Swaminath Bharadwaj, Nico F. A. van der Vegt
Summary: Our study investigates the impact of TMAO on the solvation of nonpolar solutes in water through MD simulations and free-energy calculations. We find that TMAO can exhibit a surfactant-like behavior, preferring to bind to large solutes and reducing the free-energy cost of solute-cavity formation. This behavior reinforces the solvent-mediated attraction between large solutes by means of an entropic force related to the accumulation of TMAO at interfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Renan Vergara, Tania Berrocal, Eva Isela Juarez Mejia, Sergio Romero-Romero, Isabel Velazquez-Lopez, Nancy O. Pulido, Haven A. Lopez A. Sanchez, Daniel-Adriano Silva, Miguel Costas, Adela Rodriguez-Romero, Rogelio Rodriguez-Sotres, Alejandro Sosa-Peinado, D. Alejandro Fernandez-Velasco
Summary: This article describes the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. The results reveal unexpected behavior of the continuous and discontinuous domains, indicating the crucial role of the continuous domain in nucleating folding.
Article
Biochemistry & Molecular Biology
Zully Mora-Sierra, Gopika Gopan, Roger Chang, Deborah E. Leckband, Martin Gruebele
Summary: Research demonstrates that interactions with end-grafted PNIPAM films above the lower critical solution temperature (LCST) can increase the folding stability of enzymes, such as phosphoglycerate kinase (PGK). By comparing two protein mutants, it is found that protein adsorption on different densities of PNIPAM affects stabilization. Additionally, experiments on temperature-dependent kinetics suggest that PNIPAM mainly interacts with the protein surface to increase conformational entropy, rather than crowding the unfolded state of the protein.
Article
Biochemistry & Molecular Biology
Kristin Oepen, Veronika Mater, Dirk Schneider
Summary: The unfolding of proteins can be studied by introducing urea, but this method doesn't work for membrane integral protein domains. However, the addition of sodium dodecyl sulfate can induce unfolding of alpha-helical membrane proteins. Monitoring changes in Trp fluorescence is limited in studying the folding and stability of individual domains in multi-domain membrane proteins. In this study, the unfolding and stability of the bacterial ABC transporter BmrA was investigated by mutating existing Trp residues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Chiung-Fang Hsu, Kai-Chun Chang, Yi-Lan Chen, Po-Szu Hsieh, An- Lee, Jui-Yun Tu, Yu-Ting Chen, Jin-Der Wen
Summary: Programmed-1 ribosomal frameshifting in viruses and bacteria is stimulated by mRNA structures within the coding region. The RNA pseudoknot folds sequentially through upstream stem S1 and downstream stem S2, with S2 tending to be trapped in intermediates. Masking nucleotides can modulate mRNA refolding and facilitate the stable folding of native pseudoknots.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Phuong Thuy Bui, Trinh Xuan Hoang
Summary: The ribosomal exit tunnel is crucial for the release of nascent proteins and shows conservation and differentiation in structure and properties across different species. This study reveals that the escape process of proteins at the ribosomal exit tunnel follows a diffusion mechanism, and the time taken for escape is influenced by the number of hydrophobic residues and net charge of the protein. The study also demonstrates quantitative differences in protein escape times due to variations in the physico-chemical properties of the tunnels.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biophysics
Cristina Paissoni, Sarita Puri, Iren Wang, Szu-Yu Chen, Carlo Camilloni, Shang-Te Danny Hsu
Summary: MJ0366 from Methanocaldococcus jannaschii is the smallest topologically knotted protein known to date, tying a trefoil knot by threading its C-terminal helix through a buttonhole formed by the remainder of the secondary structure elements. Experimental and computational results show that, despite the small size, the transition state of MJ0366 is formed at a very late stage of the folding reaction coordinate, following a polarized pathway.
BIOPHYSICAL JOURNAL
(2021)
Article
Mathematics
Marisa Kaewsuwan, Rachanee Phuwapathanapun, Weerawat Sudsutad, Jehad Alzabut, Chatthai Thaiprayoon, Jutarat Kongson
Summary: In this paper, we establish the existence and stability results for the (ρ(k),φ(k))-Hilfer fractional integro-differential equations under instantaneous impulse with non-local multi-point fractional integral boundary conditions. We achieve the formulation of the solution to the (ρ(k),φ(k))-Hilfer fractional differential equation with constant coefficients in term of the Mittag-Leffler kernel. The uniqueness result is proved by applying Banach's fixed point theory with the Mittag-Leffler properties, and the existence result is derived by using a fixed point theorem due to O'Regan. Furthermore, Ulam-Hyers stability and Ulam-Hyers-Rassias stability results are demonstrated via the non-linear functional analysis method. In addition, numerical examples are designed to demonstrate the application of the main results.