We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.
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http://dx.doi.org/10.1021/ac048661s | DOI Listing |
Int J Biol Macromol
December 2024
Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China. Electronic address:
Thermostability is a key factor for the industrial application of enzymes. This review categorizes enzymes by their applications and discusses the importance of engineering thermostability for practical use. It summarizes fundamental theories and recent advancements in enzyme thermostability modification, including directed evolution, semi-rational design, and rational design.
View Article and Find Full Text PDFJ Chem Theory Comput
December 2024
School of Pharmaceutical Sciences and Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Rue Michel Servet 1, 1206 Genève, Switzerland.
We introduce an enhanced sampling algorithm to obtain converged free energy landscapes of molecular rare events, even when the collective variable (CV) used for biasing is not optimal. Our approach samples a time-dependent target distribution by combining the on-the-fly probability enhanced sampling and its exploratory variant, OPES Explore. This promotes more transitions between the relevant metastable states and accelerates the convergence speed of the free energy estimate.
View Article and Find Full Text PDFMembranes (Basel)
November 2024
Department of Biochemistry, University of Illinois Urbana, Champaign, IL 61801, USA.
Protein-lipid interactions demonstrate important regulatory roles in the function of membrane proteins. Nevertheless, due to the semi-liquid nature and heterogeneity of biological membranes, and dissecting the details of such interactions at high resolutions continues to pose a major challenge to experimental biophysical techniques. Computational techniques such as molecular dynamics (MD) offer an alternative approach with both temporally and spatially high resolutions.
View Article and Find Full Text PDFJ Fungi (Basel)
December 2024
Division of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
Hyaluronidases have been a subject of great interest in medical and cosmeceutical applications. Previously, our group demonstrated that the venom glands of contain hyaluronidase enzymes (VesT2s), and heterologous expression of the corresponding gene () in systems results in inclusion bodies, necessitating functional folding using urea. Here, we report the successful heterologous expression of VesT2a in the expression system, with gene construction achieved using Golden.
View Article and Find Full Text PDFPNAS Nexus
January 2025
School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA.
Recombinant antibodies are a promising class of therapeutics to treat protein misfolding associated with neurodegenerative diseases, and several antibodies that inhibit aggregation are approved or in clinical trials to treat Alzheimer's disease. Here, we developed antibodies targeting the aggregation-prone β-propeller olfactomedin (OLF) domain of myocilin, variants of which comprise the strongest genetic link to glaucoma and cause early onset vision loss for several million individuals worldwide. Mutant myocilin aggregates intracellularly in the endoplasmic reticulum (ER).
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