Publications by authors named "A M Gronenborn"

471 Publications

Integrative structural biology of HIV-1 capsid protein assemblies: combining experiment and computation.

Curr Opin Virol 2021 Apr 23;48:57-64. Epub 2021 Apr 23.

University of Delaware, Department of Chemistry and Biochemistry, Newark, DE, United States; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States. Electronic address:

HIV-1 is the causative agent of acquired immunodeficiency syndrome (AIDS), a global pandemic that has claimed 32.7 million lives since 1981. Despite decades of research, there is no cure for the disease, with 38 million people currently infected with HIV. Attractive therapeutic targets for drug development are mature HIV-1 capsids, immature Gag polyprotein assemblies, and Gag maturation intermediates, although their complex architectures, pleomorphism, and dynamics render these assemblies challenging for structural biology. The recent development of integrative approaches, combining experimental and computational methods has enabled atomic-level characterization of structures and dynamics of capsid and Gag assemblies, and revealed their interactions with small-molecule inhibitors and host factors. These structures provide important insights that will guide the development of capsid and maturation inhibitors.
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http://dx.doi.org/10.1016/j.coviro.2021.03.005DOI Listing
April 2021

Assessing the Structures and Interactions of γD-Crystallin Deamidation Variants.

Structure 2021 Mar 1;29(3):284-291.e3. Epub 2020 Dec 1.

Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15261, USA. Electronic address:

Cataracts involve the deposition of the crystallin proteins in the vertebrate eye lens, causing opacification and blindness. They are associated with either genetic mutation or protein damage that accumulates over the lifetime of the organism. Deamidation of Asn residues in several different crystallins has been observed and is frequently invoked as a cause of cataract. Here, we investigated the properties of Asp variants, deamidation products of γD-crystallin, by solution NMR, X-ray crystallography, and other biophysical techniques. No substantive structural or stability changes were noted for all seven Asn to Asp γD-crystallins. Importantly, no changes in diffusion interaction behavior could be detected. Our combined experimental results demonstrate that introduction of single Asp residues on the surface of γD-crystallin by deamidation is unlikely to be the driver of cataract formation in the eye lens.
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http://dx.doi.org/10.1016/j.str.2020.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935750PMC
March 2021

A detailed picture of a protein-carbohydrate hydrogen-bonding network revealed by NMR and MD simulations.

Glycobiology 2021 May;31(4):508-518

Department of Structural Biology, University of Pittsburgh School of Medicine,1051 BST3, 3501 Fifth Ave, Pittsburgh, PA 15261, USA.

Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.
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http://dx.doi.org/10.1093/glycob/cwaa081DOI Listing
May 2021

Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.

Nat Struct Mol Biol 2020 09 8;27(9):863-869. Epub 2020 Sep 8.

Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.

HIV-1 capsid plays multiple key roles in viral replication, and inhibition of capsid assembly is an attractive target for therapeutic intervention. Here, we report the atomic-resolution structure of capsid protein (CA) tubes, determined by magic-angle spinning NMR and data-guided molecular dynamics simulations. Functionally important regions, including the NTD β-hairpin, the cyclophilin A-binding loop, residues in the hexamer central pore, and the NTD-CTD linker region, are well defined. The structure of individual CA chains, their arrangement in the pseudo-hexameric units of the tube and the inter-hexamer interfaces are consistent with those in intact capsids and substantially different from the organization in crystal structures, which feature flat hexamers. The inherent curvature in the CA tubes is controlled by conformational variability of residues in the linker region and of dimer and trimer interfaces. The present structure reveals atomic-level detail in capsid architecture and provides important guidance for the design of novel capsid inhibitors.
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http://dx.doi.org/10.1038/s41594-020-0489-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7490828PMC
September 2020

Accurate Backbone C and N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.

Chemphyschem 2020 07 4;21(13):1436-1443. Epub 2020 Jun 4.

Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States.

Chemical shift tensors obtained from solid-state NMR spectroscopy are very sensitive reporters of structure and dynamics in proteins. While accurate C and N chemical shift tensors are accessible by magic angle spinning (MAS) NMR, their quantum mechanical calculations remain challenging, particularly for N atoms. Here we compare experimentally determined backbone C and N chemical shift tensors by MAS NMR with hybrid quantum mechanics/molecular mechanics/molecular dynamics (MD-QM/MM) calculations for the carbohydrate-binding domain of galectin-3. Excellent agreement between experimental and computed N chemical shift anisotropy values was obtained using the Amber ff15ipq force field when solvent dynamics was taken into account in the calculation. Our results establish important benchmark conditions for improving the accuracy of chemical shift calculations in proteins and may aid in the validation of protein structure models derived by MAS NMR.
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http://dx.doi.org/10.1002/cphc.202000249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8080305PMC
July 2020