Stabilization of the metastable envelope glycoprotein (Env) of HIV-1 is hypothesized to improve induction of broadly neutralizing antibodies. We improved the expression yield and stability of the HIV-1 envelope glycoprotein BG505SOSIP.664 gp140 by means of a previously described automated sequence and structure-guided computational thermostabilization approach, PROSS. This combines sequence conservation information with computational assessment of mutant stabilization, thus taking advantage of the extensive natural sequence variation present in HIV-1 Env. PROSS is used to design three gp140 variants with 17-45 mutations relative to the parental construct. One of the designs is experimentally observed to have a fourfold improvement in yield and a 4 °C increment in thermostability. In addition, the designed immunogens have similar antigenicity profiles to the native flexible linker version of wild type, BG505SOSIP.664 gp140 (NFL Wt) to major epitopes targeted by broadly neutralizing antibodies. PROSS eliminates the laborious process of screening many variants for stability and functionality, providing a proof of principle of the method for stabilization and improvement of yield without compromising antigenicity for next generation complex, highly glycosylated vaccine candidates.
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http://dx.doi.org/10.1016/j.crstbi.2020.04.001 | DOI Listing |
Biosens Bioelectron
March 2025
Teaching and Research Office of Food Safety, School of Public Course, Bengbu Medical College, Bengbu, 233000, China. Electronic address:
The construction of structure-guided aptamers and the ultra-sensitive aptamer-based lateral flow assays (Apt-LFA) integrated detection method hold significant potential for food analysis. Using an engineered modified sequence strategy, we successfully developed the aptamer Cap-1-2M4, significantly enhancing its affinity for capsaicin (CAP) to 0.6197 ± 0.
View Article and Find Full Text PDFbioRxiv
November 2024
Biomedical Science graduate program, School of Medicine, University of California at San Diego.
Proteins with nuclear localization sequences (NLSs) are directed into the cell nucleus through interactions between the NLS and importin proteins. NLSs are generally short motifs rich in basic amino acids; however, identifying NLSs can be challenging due to the lack of a universally conserved sequence. In this study, we characterized the sequence specificity of an essential and conserved NLS in Mcm3, a subunit of the replicative DNA helicase.
View Article and Find Full Text PDFJ Cheminform
November 2024
MOE Key Laboratory of Bioinformatics, State Key Laboratory of Molecular Oncology, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
Predicting protein-small molecule binding sites, the initial step in structure-guided drug design, remains challenging for proteins lacking experimentally derived ligand-bound structures. Here, we propose CLAPE-SMB, which integrates a pre-trained protein language model with contrastive learning to provide high accuracy predictions of small molecule binding sites that can accommodate proteins without a published crystal structure. We trained and tested CLAPE-SMB on the SJC dataset, a non-redundant dataset based on sc-PDB, JOINED, and COACH420, and achieved an MCC of 0.
View Article and Find Full Text PDFNat Comput Sci
November 2024
Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
RNAs represent a class of programmable biomolecules capable of performing diverse biological functions. Recent studies have developed accurate RNA three-dimensional structure prediction methods, which may enable new RNAs to be designed in a structure-guided manner. Here, we develop a structure-to-sequence deep learning platform for the de novo generative design of RNA aptamers.
View Article and Find Full Text PDFStructure
January 2025
RNAP Laboratory, Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK. Electronic address:
N-utilization substance A (NusA) is a regulatory factor with pleiotropic functions in gene expression in bacteria. Archaea encode two conserved small proteins, NusA1 and NusA2, with domains orthologous to the two RNA binding K Homology (KH) domains of NusA. Here, we report the crystal structures of NusA2 from Sulfolobus acidocaldarius and Saccharolobus solfataricus obtained at 3.
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