In response to the growth of emerging resistance to conventional antifungal drugs, antifungal proteins (AFPs) of filamentous Ascomycetes origin have been discovered in recent years. Understanding the structure of AFPs is crucial for elucidating their antifungal mechanisms and developing new therapeutic agents. While nuclear magnetic resonance (NMR) has proven effective in determining the structures of small proteins, some AFP structures remain unresolved, necessitating the use of alternative...
[NMR paper] Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics
Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics
The advent of accurate methods to predict the fold of proteins initiated by AlphaFold2 is rapidly changing our understanding of proteins and helping their design. However, these methods are mainly trained on protein structures determined with X-ray diffraction, where the protein is packed in crystals at often cryogenic temperatures. They can therefore only reliably cover well-folded parts of proteins that experience few, if any, conformational changes....
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[NMR paper] Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data
Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data
Plastocyanin is a small mobile protein that facilitates electron transfer through the formation of short-lived protein-protein complexes with cytochrome bf and photosystem 1. Due to the transient nature of plastocyanin-cytochrome f complex, the lack of a long-lived tight complex makes it impossible to determine its structure by X-ray diffraction analysis. Up to today, a number of slightly different structures of such complexes have been obtained by...
[NMR paper] Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data
Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data
Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been...
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06-01-2023 05:37 PM
[NMR paper] Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data
Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data
Recent advances in molecular modeling of protein structures are changing the field of structural biology. AlphaFold-2 (AF2), an AI system developed by DeepMind, Inc., utilizes attention-based deep learning to predict models of protein structures with high accuracy relative to structures determined by X-ray crystallography and cryo-electron microscopy (cryoEM). Comparing AF2 models to structures determined using solution NMR data, both high similarities and distinct differences have been...
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02-01-2023 06:19 AM
[NMR paper] DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study
DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study
PAF and related antifungal proteins are promising antimicrobial agents. They have highly stable folds around room temperature due to the presence of 3-4 disulfide bonds. However, unfolded states persist and contribute to the thermal equilibrium in aqueous solution, and low-populated states might influence their biological impact. To explore such equilibria during dimethyl sulfoxide (DMSO)-induced chemical unfolding, we studied PAF and its inactive variant PAF^(D19S) using...
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01-21-2023 04:42 PM
[NMR paper] AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures
AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR and cryo-electron microscopy structures. Here we assess the hypothesis that AlphaFold models of small, relatively rigid proteins have accuracies...
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06-30-2022 11:57 AM
[NMR paper] "Invisible" Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations.
"Invisible" Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations.
Related Articles "Invisible" Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding, CEST-NMR Experiments, and Molecular Dynamics Calculations.
Chemistry. 2015 Feb 12;
Authors: Fizil Á, Gáspári Z, Barna T, Marx F, Batta G
Abstract
Transition between conformational states in proteins is being recognized as a possible key factor...
Small Disulfide Proteins with Antifungal Impact: NMR Experimental Structures as Compared to Models of Alphafold Versions
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