Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

Journal Browser

From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (28 September 2021) | Viewed by 23105

Share This Special Issue

Special Issue Editor

Dr. Christof Lenz

E-Mail Website
Guest Editor

Institute of Clinical Chemistry, University Medical Center Goettingen，Goettingen, Germany
Interests: mass spectrometry; proteomics; clinical research; tissue proteomics

Special Issue Information

Dear Colleagues,

Biomolecular complexes are at the heart of almost all cellular events. Proteins especially interact with other proteins, but also with DNA, RNA or metabolites, to deliver biological function in a tightly controlled manner. A range of methods employing mass spectrometry have been developed to study these interactions and their spatial, temporal and functional changes. In combination with dedicated biochemical workflows and specific enrichment and separation schemes, mass spectrometry, as a largely unbiased technology, has allowed us to greatly improve our understanding of how biomolecular complexes are organized and how they contribute to cellular processes.

I would like to invite you to celebrate these improvements by contributing to the IJMS Special Issue “From affinity to proximity to interaction: mass spectrometry methods to study biomolecular complexes”. This open access Special Issue will bring together original research and review articles, especially in the fields of interactomics, proximity proteomics and complexome profiling. Other topics may include the study of protein/oligonucleotide complexes, or approaches utilizing analytical approaches complementary to mass spectrometric detection.

I am very much looking forward to your contributions!

Dr. Christof Lenz
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

pnon-covalent interactions
protein/protein complexes
affinity purification mass spectrometry
interactome
proximity labeling
complexome profiling

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (6 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

24 pages, 4301 KiB

Open AccessArticle

A Multi-Perspective Proximity View on the Dynamic Head Region of the Ribosomal 40S Subunit

by Kerstin Schmitt, Alina-Andrea Kraft and Oliver Valerius

Int. J. Mol. Sci. 2021, 22(21), 11653; https://doi.org/10.3390/ijms222111653 - 28 Oct 2021

Cited by 3 | Viewed by 3330

Abstract

A comparison of overlapping proximity captures at the head region of the ribosomal 40S subunit (hr40S) in Saccharomyces cerevisiae from four adjacent perspectives, namely Asc1/RACK1, Rps2/uS5, Rps3/uS3, and Rps20/uS10, corroborates dynamic co-localization of proteins that control activity and fate of both ribosomes and mRNA. Co-locating factors that associate with the hr40S are involved in (i) (de)ubiquitination of ribosomal proteins (Hel2, Bre5-Ubp3), (ii) clamping of inactive ribosomal subunits (Stm1), (iii) mRNA surveillance and vesicular transport (Smy2, Syh1), (iv) degradation of mRNA (endo- and exonucleases Ypl199c and Xrn1, respectively), (v) autophagy (Psp2, Vps30, Ykt6), and (vi) kinase signaling (Ste20). Additionally, they must be harmonized with translation initiation factors (eIF3, cap-binding protein Cdc33, eIF2A) and mRNA-binding/ribosome-charging proteins (Scp160, Sro9). The Rps/uS-BioID perspectives revealed substantial Asc1/RACK1-dependent hr40S configuration indicating a function of the β-propeller in context-specific spatial organization of this microenvironment. Toward resolving context-specific constellations, a Split-TurboID analysis emphasized the ubiquitin-associated factors Def1 and Lsm12 as neighbors of Bre5 at hr40S. These shuttling proteins indicate a common regulatory axis for the fate of polymerizing machineries for the biosynthesis of proteins in the cytoplasm and RNA/DNA in the nucleus. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Figure 1

14 pages, 2469 KiB

Open AccessArticle

Butyrylcholinesterase–Protein Interactions in Human Serum

by Jacek Jasiecki, Anna Szczoczarz, Dominik Cysewski, Krzysztof Lewandowski, Piotr Skowron, Krzysztof Waleron and Bartosz Wasąg

Int. J. Mol. Sci. 2021, 22(19), 10662; https://doi.org/10.3390/ijms221910662 - 1 Oct 2021

Cited by 15 | Viewed by 3172

Abstract

Measuring various biochemical and cellular components in the blood is a routine procedure in clinical practice. Human serum contains hundreds of diverse proteins secreted from all cells and tissues in healthy and diseased states. Moreover, some serum proteins have specific strong interactions with other blood components, but most interactions are probably weak and transient. One of the serum proteins is butyrylcholinesterase (BChE), an enzyme existing mainly as a glycosylated soluble tetramer that plays an important role in the metabolism of many drugs. Our results suggest that BChE interacts with plasma proteins and forms much larger complexes than predicted from the molecular weight of the BChE tetramer. To investigate and isolate such complexes, we developed a two-step strategy to find specific protein–protein interactions by combining native size-exclusion chromatography (SEC) with affinity chromatography with the resin that specifically binds BChE. Second, to confirm protein complexes′ specificity, we fractionated blood serum proteins by density gradient ultracentrifugation followed by co-immunoprecipitation with anti-BChE monoclonal antibodies. The proteins coisolated in complexes with BChE were identified by mass spectroscopy. These binding studies revealed that BChE interacts with a number of proteins in the human serum. Some of these interactions seem to be more stable than transient. BChE copurification with ApoA-I and the density of some fractions containing BChE corresponding to high-density lipoprotein cholesterol (HDL) during ultracentrifugation suggest its interactions with HDL. Moreover, we observed lower BChE plasma activity in individuals with severely reduced HDL levels (≤20 mg/dL). The presented two-step methodology for determination of the BChE interactions can facilitate further analysis of such complexes, especially from the brain tissue, where BChE could be involved in the pathogenesis and progression of AD. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Figure 1

Review

Jump to: Research

25 pages, 5047 KiB

Open AccessReview

Unravel the Local Complexity of Biological Environments by MALDI Mass Spectrometry Imaging

by Elvira Sgobba, Yohann Daguerre and Marco Giampà

Int. J. Mol. Sci. 2021, 22(22), 12393; https://doi.org/10.3390/ijms222212393 - 17 Nov 2021

Cited by 12 | Viewed by 4037

Abstract

Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Figure 1

12 pages, 5245 KiB

Open AccessReview

Complexome Profiling: Assembly and Remodeling of Protein Complexes

by Ilka Wittig and Pedro Felipe Malacarne

Int. J. Mol. Sci. 2021, 22(15), 7809; https://doi.org/10.3390/ijms22157809 - 21 Jul 2021

Cited by 19 | Viewed by 3830

Abstract

Many proteins have been found to operate in a complex with various biomolecules such as proteins, nucleic acids, carbohydrates, or lipids. Protein complexes can be transient, stable or dynamic and their association is controlled under variable cellular conditions. Complexome profiling is a recently developed mass spectrometry-based method that combines mild separation techniques, native gel electrophoresis, and density gradient centrifugation with quantitative mass spectrometry to generate inventories of protein assemblies within a cell or subcellular fraction. This review summarizes applications of complexome profiling with respect to assembly ranging from single subunits to large macromolecular complexes, as well as their stability, and remodeling in health and disease. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Figure 1

13 pages, 995 KiB

Open AccessReview

From Affinity to Proximity Techniques to Investigate Protein Complexes in Plants

by Sandra M. Kerbler, Roberto Natale, Alisdair R. Fernie and Youjun Zhang

Int. J. Mol. Sci. 2021, 22(13), 7101; https://doi.org/10.3390/ijms22137101 - 1 Jul 2021

Cited by 10 | Viewed by 4088

Abstract

The study of protein–protein interactions (PPIs) is fundamental in understanding the unique role of proteins within cells and their contribution to complex biological systems. While the toolkit to study PPIs has grown immensely in mammalian and unicellular eukaryote systems over recent years, application of these techniques in plants remains under-utilized. Affinity purification coupled to mass spectrometry (AP-MS) and proximity labeling coupled to mass spectrometry (PL-MS) are two powerful techniques that have significantly enhanced our understanding of PPIs. Relying on the specific binding properties of a protein to an immobilized ligand, AP is a fast, sensitive and targeted approach used to detect interactions between bait (protein of interest) and prey (interacting partners) under near-physiological conditions. Similarly, PL, which utilizes the close proximity of proteins to identify potential interacting partners, has the ability to detect transient or hydrophobic interactions under native conditions. Combined, these techniques have the potential to reveal an unprecedented spatial and temporal protein interaction network that better understands biological processes relevant to many fields of interest. In this review, we summarize the advantages and disadvantages of two increasingly common PPI determination techniques: AP-MS and PL-MS and discuss their important application to plant systems. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Figure 1

14 pages, 945 KiB

Open AccessReview

Discovery–Versus Hypothesis–Driven Detection of Protein–Protein Interactions and Complexes

by Isabell Bludau

Int. J. Mol. Sci. 2021, 22(9), 4450; https://doi.org/10.3390/ijms22094450 - 24 Apr 2021

Cited by 8 | Viewed by 3502

Abstract

Protein complexes are the main functional modules in the cell that coordinate and perform the vast majority of molecular functions. The main approaches to identify and quantify the interactome to date are based on mass spectrometry (MS). Here I summarize the benefits and limitations of different MS-based interactome screens, with a focus on untargeted interactome acquisition, such as co-fractionation MS. Specific emphasis is given to the discussion of discovery- versus hypothesis-driven data analysis concepts and their applicability to large, proteome-wide interactome screens. Hypothesis-driven analysis approaches, i.e., complex- or network-centric, are highlighted as promising strategies for comparative studies. While these approaches require prior information from public databases, also reviewed herein, the available wealth of interactomic data continuously increases, thereby providing more exhaustive information for future studies. Finally, guidance on the selection of interactome acquisition and analysis methods is provided to aid the reader in the design of protein-protein interaction studies. Full article

(This article belongs to the Special Issue From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes)

► Show Figures

Journal Menu

Journal Browser

From Affinity to Proximity to Interaction: Mass Spectrometry Methods to Study Biomolecular Complexes

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (6 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI