Proteome sequencing goes deep

Richards, Alicia; Merrill, Anna E.; Coon, Joshua J.

doi:10.1016/j.cbpa.2014.10.017

Cited by 104 publications

(96 citation statements)

References 58 publications

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“…A crosslink contact also contains (relatively low resolution) spatial information in itself. Recent technological advances [53,54] have now rendered this method applicable to physiologically important biological assemblies that are difficult to examine using more traditional structural techniques. This technology is therefore optimally suited for studying the architecture of large protein complexes and their interaction partners in their native environment and on a medium to large scale.…”

Section: Recent Advances In Xl-ms Methodsologymentioning

confidence: 99%

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Leitner

Faini

Stengel

et al. 2016

Trends in Biochemical Sciences

349

285

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In recent years, chemical crosslinking of protein complexes and the identification of crosslinked residues by mass spectrometry (XL-MS; sometimes abbreviated as CX-MS) has become an important technique bridging mass spectrometry (MS) and structural biology. By now, XL-MS is well established and supported by publicly available resources as a convenient and versatile part of the structural biologist's toolbox. The combination of XL-MS with cryoelectron microscopy (cryo-EM) and/or integrative modeling is particularly promising to study the topology and structure of large protein assemblies. Among the targets studied so far are proteasomes, ribosomes, polymerases, chromatin remodelers, and photosystem complexes. Here we provide an overview of recent advances in XL-MS, the current state of the field, and a cursory outlook on future challenges. Chemical Crosslinking as a Tool for Structural BiologyStructural biology makes use of many different techniques to elucidate the 3D structures of proteins and protein complexes. While high-resolution structures have traditionally been obtained by X-ray crystallography, cryo-EM is increasingly able to also generate (near) atomic-resolution models. In recent years, techniques and applications of MS have also rapidly progressed. Earlier studies were largely focused on the large-scale identification and quantification of proteins, whereas recent methods also support queries into the composition, stoichiometry, and spatial arrangement of subunits in a complex. These developments have now further progressed toward generating information that contributes, as part of hybrid structural strategies, to the structure elucidation of large molecular assemblies including protein complexes that perform essential processes in the cell. XL-MS is a particularly powerful mass spectrometric technique in this respect, because it provides several layers of information. Identifying protein-protein contacts through XL-MS confirms physical proximity between subunits because the proteins must be close enough in space to be crosslinked. Localizing the side chains that are connected restricts this proximity to certain regions (e.g., domains or even single helices or loops). Finally, the structure of the connected side chains and the crosslinker moiety impart a distance restraint that can be used for molecular modeling purposes because an upper Trends Chemical crosslinking followed by the mass spectrometric analysis of cross linked peptides (XL MS) identifies con tact sites between residues within a single or between multiple proteins.The application of XL MS to many bio logically relevant molecular machines has been shown, with a rapidly growing number of successful studies reported in the past 2 3 years.Crosslinking data are useful in integra tive modeling workflows by providing distance restraints on the surface of folded proteins and complexes. XL MS has been shown to be particularly powerful in combination with 3D cryo electron microscopy. Sciences ; 41 (2016), 1. -S. 20-32 https://dx.doi.org/10.1016...

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Section: Recent Advances In Xl-ms Methodsologymentioning

confidence: 99%

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Leitner

Faini

Stengel

et al. 2016

Trends in Biochemical Sciences

349

285

View full text Add to dashboard Cite

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“…Comprehensive studies on the proteomes of cells, tissues, or organisms have been reported (e.g. Addona et al , 2009; Nilsson et al , 2010; Beck et al , 2011; Nagaraj et al , 2011; for review, see Bensimon et al , 2012; Kulak et al , 2014; Wilhelm et al , 2014; Hein et al , 2015; Richards et al , 2015), but accurate quantitative information on proteins expressed at low levels remains scarce. As a consequence, published estimates for the abundance of specific proteins sometimes vary over several orders of magnitude.…”

Section: Introductionmentioning

confidence: 99%

Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging

et al. 2016

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Centrioles are essential for the formation of centrosomes and cilia. While numerical and/or structural centrosomes aberrations are implicated in cancer, mutations in centriolar and centrosomal proteins are genetically linked to ciliopathies, microcephaly, and dwarfism. The evolutionarily conserved mechanisms underlying centrosome biogenesis are centered on a set of key proteins, including Plk4, Sas‐6, and STIL, whose exact levels are critical to ensure accurate reproduction of centrioles during cell cycle progression. However, neither the intracellular levels of centrosomal proteins nor their stoichiometry within centrosomes is presently known. Here, we have used two complementary approaches, targeted proteomics and EGFP‐tagging of centrosomal proteins at endogenous loci, to measure protein abundance in cultured human cells and purified centrosomes. Our results provide a first assessment of the absolute and relative amounts of major components of the human centrosome. Specifically, they predict that human centriolar cartwheels comprise up to 16 stacked hubs and 1 molecule of STIL for every dimer of Sas‐6. This type of quantitative information will help guide future studies of the molecular basis of centrosome assembly and function.

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“…Many of these have been aided by developments in mass spectrometry (MS)-based analysis, enabling higher sensitivity and a higher dynamic range of quantification. (23)(24)(25)(26) In addition, over the past decade, biochemical and cell biological fractionation, such as chromatography or centrifugationbased separations, have increased in efficiency and resolution. Thus, multiple separations can now more easily be combined for sequential multidimensional proteome analysis ( Figure 3).…”

Section: Building the Foundation For Genomic In Personalized Medicinementioning

confidence: 99%

Personalized Medicine: The Future of Health Care

2016

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BACKGROUND: Most medical treatments have been designed for the "average patients." As a result of this "one-size-fits-all-approach," treatments can be very successful for some patients but not for others. The issue is shifted by the new innovation approach in diseases treatment and prevention, precision medicine, which takes into account individual differences in people's genes, environments, and lifestyles. This review was aimed to describe a new approach of healthcare performance strategy based on individual genetic variants. CONTENT:Researchers have discovered hundreds of genes that harbor variations contributing to human illness, identified genetic variability in patients' responses to different of treatments, and from there begun to target the Abstract R E V I E W A R T I C L Egenes as molecular causes of diseases. In addition, scientists are developing and using diagnostic tests based on genetics or other molecular mechanisms to better predict patients' responses to targeted therapy. SUMMARY:Personalized medicine seeks to use advances in knowledge about genetic factors and biological mechanisms of disease coupled with unique considerations of an individual's patient care needs to make healthcare more safe and effective. As a result of these contributions to improvement in the quality of care, personalized medicine represents a key strategy of healthcare reform.

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Proteome sequencing goes deep

Cited by 104 publications

References 58 publications

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines

Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging

Personalized Medicine: The Future of Health Care

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