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| http://dx.doi.org/10.1093/bioadv/vbac024 | DOI Listing |
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Benchmarking biomolecular force field-based Zn for mono- and bimetallic ligand binding sites.
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March 2023
Center for Functional Protein Assemblies (CPA), Technical University of Munich, Garching, Germany.
Zn is one of the most versatile biologically available metal ions, but accurate modeling of Zn -containing metalloproteins at the biomolecular force field level can be challenging. Since most Zn models are parameterized in bulk solvent, in-depth knowledge about their performance in a protein environment is limited. Thus, we systematically investigate here the behavior of non-polarizable Zn models for their ability to reproduce experimentally determined metal coordination and ligand binding in metalloproteins.
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February 2023
Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstr. 4, D-85747 Garching, Germany.
The cycling import receptor PEX5 and its membrane-located binding partner PEX14 are key constituents of the peroxisomal import machinery. Upon recognition of newly synthesized cargo proteins carrying a peroxisomal targeting signal type 1 (PTS1) in the cytosol, the PEX5/cargo complex docks at the peroxisomal membrane by binding to PEX14. The PEX14 N-terminal domain (NTD) recognizes (di)aromatic peptides, mostly corresponding to Wxxx(F/Y)-motifs, with nano-to micromolar affinity.
View Article and Find Full Text PDFComparison of allosteric signaling in DnaK and BiP using mutual information between simulated residue conformations.
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TUM Center for Functional Protein Assemblies and TUM School of Life Sciences, Technische Universität München, Freising, Bavaria, Germany.
The heat shock protein 70 kDa (Hsp70) chaperone system serves as a critical component of protein quality control across a wide range of prokaryotic and eukaryotic organisms. Divergent evolution and specialization to particular organelles have produced numerous Hsp70 variants which share similarities in structure and general function, but differ substantially in regulatory aspects, including conformational dynamics and activity modulation by cochaperones. The human Hsp70 variant BiP (also known as GRP78 or HSPA5) is of therapeutic interest in the context of cancer, neurodegenerative diseases, and viral infection, including for treatment of the pandemic virus SARS-CoV-2.
View Article and Find Full Text PDFDynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock.
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TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany.
Macrocycles are interesting molecules with unique features due to their conformationally constrained yet flexible ring structure. This characteristic poses a difficult challenge for computational modeling studies since they rely on accurate structural descriptions. In particular, molecular docking calculations suffer from the lack of ring flexibility during pose generation, which is often compensated by using pregenerated ligand conformer ensembles.
View Article and Find Full Text PDFInvestigation of the pH-dependent aggregation mechanisms of GCSF using low resolution protein characterization techniques and advanced molecular dynamics simulations.
Comput Struct Biotechnol J
March 2022
Technical University of Denmark, Department of Chemistry, 2800 Kongens Lyngby, Denmark.
Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0.
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