Despite the large and complex conformational space available to an unfolded protein, many small globular proteins fold with simple two-state cooperative kinetics. Understanding what determines folding rates beyond simple rules summarizing kinetic trends has proved to be more elusive than predicting folding mechanism. Topology-based models with smooth energy landscapes give reasonable predictions of the structure of the transition state ensemble, but do not have the kinetic or thermodynamic cooperativity exhibited by two-state proteins. This review outlines some recent efforts to understand what determines the cooperativity and the diversity of folding rates of two-state folding proteins.
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http://dx.doi.org/10.1016/j.sbi.2009.12.013 | DOI Listing |
Nat Commun
January 2025
Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India.
Single-point mutations are pivotal in molecular zoology, shaping functions and influencing genetic diversity and evolution. Here we study three such genetic variants of a mechano-responsive protein, cadherin-23, that uphold the structural integrity of the protein, but showcase distinct genotypes and phenotypes. The variants exhibit subtle differences in transient intra-domain interactions, which in turn affect the anti-correlated motions among the constituent β-strands.
View Article and Find Full Text PDFDev Reprod
December 2024
Kidang Marine Science Institute, Jeju National University, Jeju 63333, Korea.
This study investigated the progressive morphological alterations and digestive tract development in larval and juvenile red spotted grouper, across growth stages. External shape observations were made using an optical microscope, and the development of the digestive tract was investigated using histological methods. At 1 day after hatching (DAH), the digestive tract appeared as a straight tube extending between the ventral side and yolk-sac.
View Article and Find Full Text PDFEnzyme Microb Technol
January 2025
Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Building 221, Technical University of Denmark, Lyngby DK-2800 Kgs, Denmark. Electronic address:
Aspergillus spp. and Rhizopus spp., used in solid-state plant food fermentations, encode cobalamin-independent methionine synthase activity (MetE, EC 2.
View Article and Find Full Text PDFJ Chem Phys
January 2025
Research and Development Center, Beijing Genetech Pharmaceutical Co., Ltd., Beijing 102200, People's Republic of China.
Understanding the folding mechanisms of multi-domain proteins is crucial for gaining insights into protein folding dynamics. The BphC enzyme, a key player in the degradation of polychlorinated biphenyls consists of eight identical subunits, each containing two domains, with each domain comprising two "βαβββ" motifs. In this study, we employed high-temperature molecular dynamics simulations to systematically analyze the unfolding dynamics of a BphC subunit.
View Article and Find Full Text PDFChem Commun (Camb)
January 2025
Chemistry Department, University of Central Florida, Orlando, Florida 32816, USA.
Molecular beacon (MB) probes have been extensively used for nucleic acid analysis. However, MB probes fail to hybridize with folded DNA or RNA. Here, we demonstrate that MB probes equipped with extra sequences complementary to the analyte, named 'tail', can increase the signal-to-background ratio by ∼40-fold and hybridization rates by ∼800-fold compared to conventional MB probes.
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