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 Uranyl Binding to Proteins and Structural-Functional Impacts

Biomolecules ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 457 ◽  
Author(s):  
Ying-Wu Lin
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Metal Binding ◽  
Structural Information ◽  
Metal Binding Sites ◽  
Biological Remediation ◽  
Protein Dna Interactions ◽  
Ligand Interactions ◽  
Function Relationship ◽  
Relationship Of

The widespread use of uranium for civilian purposes causes a worldwide concern of its threat to human health due to the long-lived radioactivity of uranium and the high toxicity of uranyl ion (UO22+). Although uranyl–protein/DNA interactions have been known for decades, fewer advances are made in understanding their structural-functional impacts. Instead of focusing only on the structural information, this article aims to review the recent advances in understanding the binding of uranyl to proteins in either potential, native, or artificial metal-binding sites, and the structural-functional impacts of uranyl–protein interactions, such as inducing conformational changes and disrupting protein-protein/DNA/ligand interactions. Photo-induced protein/DNA cleavages, as well as other impacts, are also highlighted. These advances shed light on the structure-function relationship of proteins, especially for metalloproteins, as impacted by uranyl–protein interactions. It is desired to seek approaches for biological remediation of uranyl ions, and ultimately make a full use of the double-edged sword of uranium.

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.

The bacterial receptor protein, transferrin-binding protein B, does not independently facilitate the release of metal ion from human transferrin

2003 ◽  
Vol 81 (4) ◽  
pp. 275-283 ◽  
Author(s):  
Ulyana Nemish ◽  
Rong-Hua Yu ◽  
Leslie W Tari ◽  
Karla Krewulak ◽  
Anthony B Schryvers
Keyword(s):  
Outer Membrane ◽  
Metal Binding ◽  
Metal Ion ◽  
Binding Protein ◽  
Protein A ◽  
Nitrilotriacetic Acid ◽  
Receptor Protein ◽  
Binding Studies ◽  
Metal Ion Removal ◽  
Protein B

Pathogenic Gram-negative bacteria of the Pasteurellaceae and Neisseriaceae acquire iron for growth from host transferrin through the action of specific surface receptors. Iron is removed from transferrin by the receptor at the cell surface and is transported across the outer membrane to the periplasm. A periplasmic binding protein-dependent pathway subsequently transports iron into the cell. The transferrin receptor is composed of a largely surface-exposed lipoprotein, transferrin binding protein B, and a TonB-dependent integral outer membrane protein, transferrin binding protein A. To examine the role of transferrin binding protein B in the iron removal process, complexes of recombinant transferrin binding protein B and transferrin were prepared and compared with transferrin in metal-binding and -removal experiments. A polyhistidine-tagged form of recombinant transferrin binding protein B was able to purify a complex with transferrin that was largely monodisperse by dynamic light scattering analysis. Gallium was used instead of iron in the metal-binding studies, since it resulted in increased stability of recombinant transferrin binding protein B in the complex. Difference absorption spectra were used to monitor removal of gallium by nitrilotriacetic acid. Kinetic and equilibrium binding studies indicated that transferrin binds gallium more tightly in the presence of transferrin binding protein B. Thus, transferrin binding protein B does not facilitate metal ion removal and additional components are required for this process.Key words: iron, transport, outer membrane, lipoprotein, glycoprotein.

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.

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 MeLAD: an integrated resource for metalloenzyme-ligand associations

2019 ◽  
Author(s):  
Gen Li ◽  
Yu Su ◽  
Yu-Hang Yan ◽  
Jia-Yi Peng ◽  
Qing-Qing Dai ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Metal Binding ◽  
Metal Ion ◽  
Structural Data ◽  
Structural Similarity ◽  
Functional Class ◽  
Supplementary Information ◽  
Biological Processes ◽  
Ligand Interactions ◽  
Data Source

Abstract Motivation Metalloenzymes are attractive targets for therapeutic intervention owing to their central roles in various biological processes and pathological situations. The fast-growing body of structural data on metalloenzyme-ligand interactions is facilitating efficient drug discovery targeting metalloenzymes. However, there remains a shortage of specific databases that can provide centralized, interconnected information exclusive to metalloenzyme-ligand associations. Results We created a Metalloenzyme-Ligand Association Database (MeLAD), which is designed to provide curated structural data and information exclusive to metalloenzyme-ligand interactions, and more uniquely, present expanded associations that are represented by metal-binding pharmacophores (MBPs), metalloenzyme structural similarity (MeSIM) and ligand chemical similarity (LigSIM). MeLAD currently contains 6086 structurally resolved interactions of 1416 metalloenzymes with 3564 ligands, of which classical metal-binding, non-classical metal-binding, non-metal-binding and metal water-bridging interactions account for 63.0%, 2.3%, 34.4% and 0.3%, respectively. A total of 263 monodentate, 191 bidentate and 15 tridentate MBP chemotypes were included in MeLAD, which are linked to different active site metal ions and coordination modes. 3726 and 52 740 deductive metalloenzyme-ligand associations by MeSIM and LigSIM analyses, respectively, were included in MeLAD. An online server is provided for users to conduct metalloenzyme profiling prediction for small molecules of interest. MeLAD is searchable by multiple criteria, e.g. metalloenzyme name, ligand identifier, functional class, bioinorganic class, metal ion and metal-containing cofactor, which will serve as a valuable, integrative data source to foster metalloenzyme related research, particularly involved in drug discovery targeting metalloenzymes. Availability and implementation MeLAD is accessible at https://melad.ddtmlab.org. Supplementary information Supplementary data are available at Bioinformatics online.

Metalloproteins: metal binding predicted on the basis of the amino acid sequence

2008 ◽  
Vol 41 (1) ◽  
pp. 104-109 ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Amino Acid ◽  
Metal Binding ◽  
Protein Sequence ◽  
Metal Ion ◽  
Single Gene ◽  
Structural Proteomics ◽  
Metal Species ◽  
Post Translational Modifications ◽  
Ion Contents ◽  
Chemical Modification Of Proteins

A protein sequence is often insufficient for knowledge of the chemical formula and the properties of the mature molecule that perform its function. Post-translational modifications are very common and most of them cannot be predicted on the basis of the protein sequence alone. A very common chemical modification of proteins that is not directly encoded by a single gene is the complexation with metal cations. Here it is shown that the uptake of metal ions (calcium, cobalt, copper, iron, magnesium, manganese, nickel or zinc) by proteins can be predicted on the basis of the amino acid composition, by using a mixture of several simplified amino acid alphabets and by employing machine learning methods, with 70–90% accuracy, depending on the type of metal. Not only is it possible to predict if a protein requires a certain metal ion but it is also possible to discriminate amongst various metal species. These results are likely to be useful in structural proteomics, by improving the experiment success rate, and in comparative genomics, where it is interesting to compare metal-ion contents in different organisms. It is particularly important that these predictions can be made when homology-based annotations are impossible.

scholarly journals Cross-linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics

2021 ◽  
Author(s):  
Christian H Ihling ◽  
Lolita Piersimoni ◽  
Marc Kipping ◽  
Andrea Sinz
Keyword(s):  
Mass Spectrometry ◽  
Cross Sections ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Ion Mobility ◽  
Hek293t Cell ◽  
Structural Proteomics ◽  
Cross Linking ◽  
E Coli ◽  
Interaction Studies

The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) Bovine serum albumin, (ii) E. coli ribosome, and (iii) HEK293T cell nuclear lysates. We identified a total of 508 unique cross-linking sites for BSA, 868 for the E. coli ribosome, and 1,623 unique cross-links for nuclear lysates, corresponding to 1,088 intra- and 535 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving 3D-structures of single proteins, but also for performing system-wide protein interaction studies.

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