Search Results - "Sgourakis, Nikolaos"
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Modeling an In-Register, Parallel “Iowa” Aβ Fibril Structure Using Solid-State NMR Data from Labeled Samples with Rosetta
Published in Structure (London) (06-01-2015)“…Determining the structures of amyloid fibrils is an important first step toward understanding the molecular basis of neurodegenerative diseases. For β-amyloid…”
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Atomic model of the type III secretion system needle
Published in Nature (London) (14-06-2012)“…The structure of the needle of the type III secretion system of Salmonella typhimurium , used to inject virulence proteins into host cells during infection,…”
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NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope
Published in Proceedings of the National Academy of Sciences - PNAS (27-01-2015)“…Significance We present an atomic-resolution structure of the M13 filamentous bacteriophage capsid, one of many filamentous viruses that play important roles…”
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High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy
Published in Nature communications (29-09-2014)“…We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall…”
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Dynamics of MHC-I molecules in the antigen processing and presentation pathway
Published in Current opinion in immunology (01-06-2021)“…•MHC-I molecules exhibit allotype-dependent conformational flexibility, which is critical for their function.•Peptide-deficient MHC-I adopt distinct groove…”
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Backbone-independent NMR resonance assignments of methyl probes in large proteins
Published in Nature communications (29-01-2021)“…Methyl-specific isotope labeling is a powerful tool to study the structure, dynamics and interactions of large proteins and protein complexes by solution-state…”
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Chemical shift-based methods in NMR structure determination
Published in Progress in nuclear magnetic resonance spectroscopy (01-06-2018)“…[Display omitted] •Ab initio fragment assembly guided by NMR chemical shifts.•Integration of chemical shifts with comparative and multi-domain modeling…”
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HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes
Published in Nature communications (10-10-2023)“…The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune…”
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TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap
Published in Nature communications (26-05-2021)“…Chaperones Tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting…”
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Programmable design of orthogonal protein heterodimers
Published in Nature (London) (01-01-2019)“…Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or…”
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De novo design of a non-local β-sheet protein with high stability and accuracy
Published in Nature structural & molecular biology (01-11-2018)“…β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo…”
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Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs
Published in Nature (London) (18-11-2021)“…The majority of oncogenic drivers are intracellular proteins, thus constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented…”
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Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms
Published in Journal of molecular biology (14-01-2011)“…Aβ(1–42) is the highly pathologic isoform of amyloid-β, the peptide constituent of fibrils and neurotoxic oligomers involved in Alzheimer's disease. Recent…”
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The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles
Published in PLoS pathogens (01-03-2013)“…The Type Three Secretion System (T3SS), or injectisome, is a macromolecular infection machinery present in many pathogenic Gram-negative bacteria. It consists…”
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Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples
Published in Proceedings of the National Academy of Sciences - PNAS (03-07-2012)“…We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse…”
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Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition
Published in Nature communications (11-12-2023)“…The conformational landscapes of peptide/human leucocyte antigen (pHLA) protein complexes encompassing tumor neoantigens provide a rationale for target…”
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High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange
Published in Nature communications (20-04-2020)“…Peptide exchange technologies are essential for the generation of pMHC-multimer libraries used to probe diverse, polyclonal TCR repertoires in various…”
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Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation
Published in Nature communications (17-09-2022)“…Loading of MHC-I molecules with peptide by the catalytic chaperone tapasin in the peptide loading complex plays a critical role in antigen presentation and…”
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A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly
Published in PLoS pathogens (01-04-2013)“…The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence…”
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Interleukin-2 druggability is modulated by global conformational transitions controlled by a helical capping switch
Published in Proceedings of the National Academy of Sciences - PNAS (31-03-2020)“…Interleukin-2 (IL-2) is a small α-helical cytokine that regulates immune cell homeostasis through its recruitment to a high-affinity heterotrimeric receptor…”
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