scholarly journals Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4133
Author(s):  
Danuta Witkowska
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Receptor Protein ◽  
Receptor Interaction ◽  
S Protein ◽  
X Ray Crystallography ◽  
Huge Impact

Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.

scholarly journals Water–protein interactions from high–resolution protein crystallography

2004 ◽  
Vol 359 (1448) ◽  
pp. 1191-1206 ◽  
Author(s):  
Masayoshi Nakasako
Keyword(s):  
Hydrogen Bond ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Water Molecules ◽  
Aqueous Environment ◽  
Hydration Water ◽  
X Ray Crystallography ◽  
Physico Chemical ◽  
Domain Motions

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

scholarly journals Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 4979
Author(s):  
Marco Giampà ◽  
Elvira Sgobba
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Noncovalent Interactions ◽  
Conformational Dynamics ◽  
High Sensitivity ◽  
Maldi Mass Spectrometry ◽  
Noncovalent Interaction ◽  
Ionization Mass ◽  
Label Free

Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.

scholarly journals Chemical Decorations of “MARs” Residents in Orchestrating Eukaryotic Gene Regulation

2020 ◽  
Vol 8 ◽  
Author(s):  
Tanaya Roychowdhury ◽  
Samit Chattopadhyay
Keyword(s):  
Gene Regulation ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Protein Function ◽  
Functional Outcomes ◽  
Three Dimensional ◽  
Limited Information ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
3D Matrix

Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.

Type I interferon structures: Possible scaffolds for the interferon-alpha receptor complex

2002 ◽  
Vol 80 (8) ◽  
pp. 1166-1173 ◽  
Author(s):  
Tattanahalli L Nagabhushan ◽  
Paul Reichert ◽  
Mark R Walter ◽  
Nicholas J Murgolo
Keyword(s):  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Type I Interferons ◽  
Dimensional Structure ◽  
Type I ◽  
Receptor Complex ◽  
X Ray Crystallography ◽  
Receptor Complexes

The structures of several type I interferons (IFNs) are known. We review the structural information known for IFN alphas and compare them to other interferons and cytokines. We also review the structural information known or proposed for IFN–cell receptor complexes. However, the structure of the IFN – cell receptor – IFN receptor2 (IFNAR2) and IFN receptor1 (IFNAR1) complex has not yet been determined. This paper describes a structural model of human IFN-IFNAR2/IFNAR1 complex using human IFN-α2b dimer as the ligand. Both the structures of recombinant human IFN-α2b and IFN-β were determined by X-ray crystallography as zinc-mediated dimers. Our proposed model was generated using human IFN-α2b dimer docked with IFNAR2/IFNAR1. We compare our model with the receptor complex models proposed for IFN-β and IFN-γ to contrast similarities and differences. The mutual binding sites of human IFN-α2b and IFNAR2/IFNAR1 complex are consistent with available mutagenesis studies.Key words: three dimensional structure, antiviral activity, receptor, interferon.

scholarly journals A Fast Lysine Cross-linker DOPA Enables Mass Spectrometry Analyses of Protein Unfolding and Weak Protein-protein Interactions

2020 ◽  
Author(s):  
Jian-Hua Wang ◽  
Yu-Liang Tang ◽  
Rohit Jain ◽  
Fan Xiao ◽  
Zhou Gong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Guanidine Hydrochloride ◽  
Rnase A ◽  
Mass Spectrometry Analysis ◽  
Cross Linking ◽  
Protein Protein Interactions ◽  
Protein Structure Analysis ◽  
Cross Linker

AbstractChemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) has become a widely used method for protein structure analysis. Central to this technology are chemical cross-linkers. The most popular cross-linkers are N-hydroxysuccinimide (NHS) esters, which react with protein amino groups relatively slowly over 10 minutes or more while in competition with the hydrolysis reaction of NHS esters. To improve the speed of cross-linking, we developed a new class of amine-selective and non-hydrolyzable di-ortho-phthalaldehyde (DOPA) cross-linkers. DOPA can cross-link proteins in 10 seconds under near physiological conditions, which is 60 times faster than the NHS ester cross-linker DSS. DOPA also works at low pH, low temperature, or in the presence of high concentrations of denaturants such as 8 M urea or 6 M guanidine hydrochloride. Further, DOPA-mediated pulse cross-linking captured the dynamic conformational changes associated with RNase A unfolding. Lastly, DOPA outperformed DSS at capturing weak but specific protein-protein interactions.

Conformational Changes In GROEL Induced by a Protein Substrate

2000 ◽  
Vol 6 (S2) ◽  
pp. 258-259
Author(s):  
S. Falke ◽  
M. Fisher ◽  
E. Gogol
Keyword(s):  
Conformational Changes ◽  
Three Dimensional ◽  
Central Cavity ◽  
En Bloc ◽  
Protein Substrate ◽  
E Coli ◽  
X Ray Crystallography ◽  
Denatured Protein ◽  
Intermediate Domain ◽  
Substrate Binding Sites

The GroEL/GroES chaperonin system of E. coli facilitates nucleotide dependent folding of select proteins. The structure of GroEL has been described by three-dimensional electron microscopy and at higher resolution by X-ray crystallography. The GroEL oligomer is a cylindrical tetradecamer composed of two heptameric rings of 57 kDa protein subunits, stacked back to back. Each subunit is comprised of two large domains, equatorial and apical, connected by a smaller intermediate domain. The intermediate “hinge” domain links the apical and equatorial domain and provides flexibility for en bloc rearrangement associated with nucleotide and GroES binding. Equatorial domains are responsible for interactions between the two heptamers and contain the ATPase activity of GroEL. Each ring of GroEL has a central cavity that is the binding site for denatured protein substrate. GroES and denatured substrate binding sites are located on the apical domains facing the central cavity.

In-Vitro Fluorescence Microscopy Studies Show Retention of Spike-Protein (SARS-Cov-2) on Cell Membrane in the Presence of Amodiaquin Dihydrochloride Dihydrate Drug

2021 ◽  
Author(s):  
Partha Pratim Mondal ◽  
Subhra Mandal
Keyword(s):  
Cell Membrane ◽  
Large Fraction ◽  
Degradation Process ◽  
Cell Receptor ◽  
Endocytic Pathway ◽  
Receptor Protein ◽  
Potential Candidate ◽  
S Protein ◽  
Cellular Environment

The ability of S-glycoprotein (S-protein) in SARS-Cov-2 to bind to the host cell receptor protein (angiotensinconverting enzyme 2 (ACE2)) leading to its entry in cellular system determines its contagious index and global spread. Three available drugs (Riboflavin, Amodiaquin dihydrochloride dihydrate (ADD) and Remidesivir) were investigated to understand the kinetics of S-protein and its entry inside a cellular environment. Optical microscopy and fluorescence-based assays on 293T cells (transfected with ACE2 plasmid) were used as the preamble for assessing the behaviour of S-protein in the presence of these drugs for the first 12 hours post S-protein - ACE2 binding. Preliminary results suggest relatively long retention of S-protein on the cell membrane in the presence of ADD drug. Evident from the %-overlap and colocalization of S-protein with endosome studies, a large fraction of S-protein entering the cell escape endosomal degradation process, suggesting S-protein takes non-endocytic mediated entry in the presence of ADD, whereas in the presence of Riboflavin, S-protein carry out normal endocytic pathway, comparable to control (no drug) group. Therefore, present study indicates ADD potentially affects S-protein’s entry mechanism (endocytic pathway) in addition to its reported target action mechanism. Hence, ADD substantially interfere with S-protein cellular entrance mechanism. However, further detailed studies at molecular scale will clarify our understanding of exact intermediate molecular processes. The present study (based on limited data) reveal ADD could be potential candidate to manage Covid-19 functions through yet unknown molecular mechanism.

scholarly journals Crystal Structure of the Human Natural Killer Cell Activating Receptor KIR2DS2 (CD158j)

2003 ◽  
Vol 197 (7) ◽  
pp. 933-938 ◽  
Author(s):  
Xavier Saulquin ◽  
Louis N. Gastinel ◽  
Eric Vivier
Keyword(s):  
T Cell ◽  
Natural Killer ◽  
Conformational Changes ◽  
Killer Cell ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Amino Acid Identity ◽  
T Cell Subsets ◽  
Dimensional Structure ◽  
Human Natural Killer Cell

Killer cell Ig-like receptors (KIRs) regulate the function of human natural killer and T cell subsets. A feature of the KIR locus is the clustering of homologous genes encoding for inhibitory and activating KIR. Inhibitory and activating KIR differ for ligand specificities and/or affinities. In particular, we show here with KIR tetramers that activating KIR2DS2 does not bind HLA-Cw3 molecules recognized by inhibitory KIR2DL2, despite 99% extracellular amino acid identity. We also report the 2.3-Å structure of KIR2DS2, which reveals subtle displacements of two residues (Tyr45 and Gln71) involved in the interaction of KIR2DL2 with HLA-Cw3. These results show that KIR molecules cannot tolerate any variability in their three-dimensional structure without altering their MHC class I recognition capacities. Therefore, the mode of recognition used by KIR largely differs from the conformational changes that characterize T cell receptor or NKG2D interaction with their respective ligands.

scholarly journals Mass Spectrometry-Based Structural Proteomics for Metal Ion/Protein Binding Studies

Biomolecules ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 135
Author(s):  
Yanchun Lin ◽  
Michael L. Gross
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Metal Binding ◽  
Metal Ion ◽  
Photochemical Oxidation ◽  
Structural Proteomics ◽  
Binding Studies ◽  
Ligand Interactions ◽  
Amino Acid Labeling

Metal ions are critical for the biological and physiological functions of many proteins. Mass spectrometry (MS)-based structural proteomics is an ever-growing field that has been adopted to study protein and metal ion interactions. Native MS offers information on metal binding and its stoichiometry. Footprinting approaches coupled with MS, including hydrogen/deuterium exchange (HDX), “fast photochemical oxidation of proteins” (FPOP) and targeted amino-acid labeling, identify binding sites and regions undergoing conformational changes. MS-based titration methods, including “protein–ligand interactions by mass spectrometry, titration and HD exchange” (PLIMSTEX) and “ligand titration, fast photochemical oxidation of proteins and mass spectrometry” (LITPOMS), afford binding stoichiometry, binding affinity, and binding order. These MS-based structural proteomics approaches, their applications to answer questions regarding metal ion protein interactions, their limitations, and recent and potential improvements are discussed here. This review serves as a demonstration of the capabilities of these tools and as an introduction to wider applications to solve other questions.

scholarly journals Structural Features of Tight-Junction Proteins

2019 ◽  
Vol 20 (23) ◽  
pp. 6020 ◽  
Author(s):  
Udo Heinemann ◽  
Anja Schuetz
Keyword(s):  
Tight Junction ◽  
Tight Junctions ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Structural Features ◽  
Resonance Spectroscopy ◽  
Tight Junction Proteins ◽  
Protein Protein Interactions ◽  
X Ray Crystallography ◽  
Junction Proteins

Tight junctions are complex supramolecular entities composed of integral membrane proteins, membrane-associated and soluble cytoplasmic proteins engaging in an intricate and dynamic system of protein–protein interactions. Three-dimensional structures of several tight-junction proteins or their isolated domains have been determined by X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy. These structures provide direct insight into molecular interactions that contribute to the formation, integrity, or function of tight junctions. In addition, the known experimental structures have allowed the modeling of ligand-binding events involving tight-junction proteins. Here, we review the published structures of tight-junction proteins. We show that these proteins are composed of a limited set of structural motifs and highlight common types of interactions between tight-junction proteins and their ligands involving these motifs.

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