The structure and function of naturally occurring proteins are governed by a large number of amino acids (≥100). The design of miniature proteins with desired structures and functions not only substantiates our knowledge about proteins but can also contribute to the development of novel applications. Excellent progress has been made towards the design of helical proteins with diverse functions. However, the development of functional β-sheet proteins remains challenging. Herein, we describe the construction and characterization of four-stranded β-sheet miniproteins made up of about 19 amino acids that bind heme inside a hydrophobic binding pocket or "heme cage" by bis-histidine coordination in an aqueous environment. The designed miniproteins bound to heme with high affinity comparable to that of native heme proteins. Atomic-resolution structures confirmed the presence of a four-stranded β-sheet fold. The heme-protein complexes also exhibited high stability against thermal and chaotrope-induced unfolding.
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http://dx.doi.org/10.1002/anie.201702472 | DOI Listing |
Comput Methods Programs Biomed
January 2025
Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Experimental Cancer Medicine, Institution for Laboratory Medicine, Karolinska Institute, 141-83 Stockholm, Sweden. Electronic address:
Background And Objective: Myeloid-derived suppressor cells (MDSCs) are a crucial and diverse group of cells found in the tumor microenvironment (TME) that facilitate progression, invasion, and metastasis within solid tumors. CD84, a homophilic adhesion molecule expressed on MDSCs, plays a critical role in their accumulation and function within the TME. This study aims to investigate the protein-protein interactions of CD84 using molecular dynamics simulations and to explore potential therapeutic strategies targeting these interactions.
View Article and Find Full Text PDFScientists are turning to AI to make antivenoms cheaper, faster, and more effective.
View Article and Find Full Text PDFChembiochem
January 2025
Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
The α-helix is an abundant and functionally important element of protein secondary structure, which has motivated intensive efforts toward chemical strategies to stabilize helical folds. One such method is the incorporation of non-canonical backbone composition through an additional methyl substituent at the C atom. Examples of monomers include the achiral 2-aminoisobutyric acid (Aib) with geminal dimethyl substitution and chiral analogues with one methyl and one non-methyl substituent.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Research Group of Cancer Biomarkers, Biomedical Research Institute of Lleida (IRBLleida), Av. Alcalde Rovira Roure, 80, 25198 Lleida, Spain.
Triple-negative breast cancer (TNBC) represents roughly one-sixth of all breast cancer patients, but accounts for 30-40% of breast cancer deaths. Due to the lack of typical biomarkers exploited clinically for breast cancer, it remains very difficult to treat. Moreover, its intrinsic high heterogeneity and proneness to become resistant to the drugs administered makes the treatment management very challenging for oncologists.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
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.
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