1
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Zou ZZ, Han MJ. Investigation of liquid chromatography-mass spectrometry analysis of a peptide aldehyde SJA6017 with identifying its hemiacetal, gem-diol, and enol ether. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5022. [PMID: 38659190 DOI: 10.1002/jms.5022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/05/2024] [Accepted: 03/08/2024] [Indexed: 04/26/2024]
Abstract
The quantitative analysis of SJA6017, a peptide aldehyde inhibitor of calpain (Calpain Inhibitor VI), has encountered challenges in preclinical drug studies. The complex reverse-phase HPLC chromatographic behavior exhibits two peaks, each containing multiple species. An liquid chromatography-mass spectrometry (LC-MS/MS) study proposed an explanation for this phenomenon, caused by the amide aldehyde structure of SJA6017. Four chemical species corresponding to the two HPLC peaks have been identified as SJA6017 and its methyl hemiacetal, methyl enol ether, and gem-diol. In many instances of preclinical studies, methanol is favored as a substitute for DMSO. The hemiacetal is formed when the amide-activated peptide aldehyde reacts with methanol, which can then be further dehydrated in the mass spectrometer ion source under high temperature to form the methyl enol ether. The hemiacetal and gem-diol can also be decomposed to SJA6017 in the ion source. Additionally, the amide-activated peptide aldehyde can easily hydrate to the gem-diol of SJA6017 during sample incubation or sample preparation. The hemiacetal and gem-diol of SJA6017 are stable enough to have different retention times in the liquid chromatography, which explains why SJA6017 appears as two peaks, each containing multiple species. An LC-MS/MS tandem quadrupole mass spectrometer quantitative analysis method is proposed, enabling the analysis of these types of samples. This work serves as both an illustrative example and a cautionary note for mass analysis, sample incubations, and sample preparations involving compounds of peptide aldehyde, including similar aldehyde-containing metabolites, especially when methanol is present. This study provides the information needed to understand peptide aldehyde behavior at various steps of preclinical in vitro studies in the presence of methanol. It has assisted in the development of the SJA6017 bioanalysis method and will also aid in the development of bioanalysis methods for similar peptide aldehydes.
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Affiliation(s)
- Zhiyang Zack Zou
- Department of DMPK, Bioanalysis & Tox, Sundia Meditech Co., Ltd, Shanghai, China
| | - Ming-Jie Han
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, Airport Economic Area, Tianjin, China
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2
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Saklani M, Jha CB, Baidya ATK, Singh S, Kumar R, Mathur R, Tiwari AK, Varshney R. Laminin mimetic angiogenic and collagen peptide hydrogel for enhance dermal wound healing. BIOMATERIALS ADVANCES 2024; 158:213761. [PMID: 38281321 DOI: 10.1016/j.bioadv.2024.213761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 01/01/2024] [Accepted: 01/06/2024] [Indexed: 01/30/2024]
Abstract
Laminins are essential in basement membrane architecture and critical in re-epithelialization and angiogenesis. These processes and collagen deposition are vital in skin wound healing. The role of angiogenic peptides in accelerating the wound-healing process has been known. The bioactive peptides could be a potential approach due to their similar effects as growth factors and inherent biocompatible and biodegradable nature with lower cost. They can also recognize ligand-receptor interaction and mimic the extracellular matrix. Here, we report novel angiogenic DYVRLAI, CDYVRLAI, angiogenic-collagen PGPIKVAV, and Ac-PGPIKVAV peptides conjugated sodium carboxymethyl cellulose hydrogel, which was designed from laminin. The designed peptide exhibits a better binding with the α3β1, αvβ3, and α5β1 integrins and CXCR2 receptor, indicating their angiogenic and collagen binding efficiency. The peptides were evaluated to stimulate wound healing in full-thickness excision wounds in normal and diabetic mice (type II). They demonstrated their efficacy in terms of angiogenesis (CD31), re-epithelialization through regeneration of the epidermis (H&E), and collagen deposition (MT). The synthesized peptide hydrogel (DYVRLAI and CDYVRLAI) showed enhanced wound contraction up to 10.1 % and 12.3 % on day 7th compared to standard becaplermin gel (49 %) in a normal wound model. The encouraging results were also observed with the diabetic model, where these peptides showed a significant decrease of 5.20 and 5.17 % in wound size on day 10th compared to the commercial gel (9.27 %). These outcomes signify that the modified angiogenic peptide is a cost effective, novel peptide motif to promote dermal wound healing in both models.
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Affiliation(s)
- Meenakshi Saklani
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Marg, Delhi 110054, Delhi, India; Babasaheb Bhimrao Ambedkar University, A Central University, Lucknow 226025, UP, India
| | - Chandan B Jha
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Marg, Delhi 110054, Delhi, India
| | - Anurag T K Baidya
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, B.H.U., Varanasi 221005, UP, India
| | - Sweta Singh
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Marg, Delhi 110054, Delhi, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, B.H.U., Varanasi 221005, UP, India
| | - Rashi Mathur
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Marg, Delhi 110054, Delhi, India
| | - Anjani K Tiwari
- Babasaheb Bhimrao Ambedkar University, A Central University, Lucknow 226025, UP, India
| | - Raunak Varshney
- Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Marg, Delhi 110054, Delhi, India.
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3
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Wang XY, Xu YM, Lau ATY. Proteogenomics in Cancer: Then and Now. J Proteome Res 2023; 22:3103-3122. [PMID: 37725793 DOI: 10.1021/acs.jproteome.3c00196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.
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Affiliation(s)
- Xiu-Yun Wang
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
| | - Andy T Y Lau
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, People's Republic of China
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4
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Howan DHO, Jenei S, Szolomajer J, Endre G, Kondorosi É, Tóth GK. Enhanced Antibacterial Activity of Substituted Derivatives of NCR169C Peptide. Int J Mol Sci 2023; 24:ijms24032694. [PMID: 36769017 PMCID: PMC9917201 DOI: 10.3390/ijms24032694] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
Medicago truncatula in symbiosis with its rhizobial bacterium partner produces more than 700 nodule-specific cysteine-rich (NCR) peptides with diverse physicochemical properties. Most of the cationic NCR peptides have antimicrobial activity and the potential to tackle antimicrobial resistance with their novel modes of action. This work focuses on the antibacterial activity of the NCR169 peptide derivatives as we previously demonstrated that the C-terminal sequence of NCR169 (NCR169C17-38) has antifungal activity, affecting the viability, morphology, and biofilm formation of various Candida species. Here, we show that NCR169C17-38 and its various substituted derivatives are also able to kill ESKAPE pathogens such as Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. The replacement of the two cysteines with serines enhanced the antimicrobial activity against most of the tested bacteria, indicating that the formation of a disulfide bridge is not required. As tryptophan can play role in the interaction with bacterial membranes and thus in antibacterial activity, we replaced the tryptophans in the NCR169C17-38C12,17/S sequence with various modified tryptophans, namely 5-methyl tryptophan, 5-fluoro tryptophan, 6-fluoro tryptophan, 7-aza tryptophan, and 5-methoxy tryptophan, in the synthesis of NCR169C17-38C12,17/S analogs. The results demonstrate that the presence of modified fluorotryptophans can significantly enhance the antimicrobial activity without notable hemolytic effect, and this finding could be beneficial for the further development of new AMPs from the members of the NCR peptide family.
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Affiliation(s)
- Dian H. O. Howan
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Sándor Jenei
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - János Szolomajer
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
| | - Gabriella Endre
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Éva Kondorosi
- Biological Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Gábor K. Tóth
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- MTA-SZTE Biomimetic Systems Research Group, Albert Szent-Györgyi Medical School, University of Szeged, H-6720 Szeged, Hungary
- Correspondence:
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5
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Deulofeu M, Peña-Méndez EM, Vaňhara P, Havel J, Moráň L, Pečinka L, Bagó-Mas A, Verdú E, Salvadó V, Boadas-Vaello P. Artificial Neural Networks Coupled with MALDI-TOF MS Serum Fingerprinting To Classify and Diagnose Pathological Pain Subtypes in Preclinical Models. ACS Chem Neurosci 2022; 14:300-311. [PMID: 36584284 PMCID: PMC9853500 DOI: 10.1021/acschemneuro.2c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Pathological pain subtypes can be classified as either neuropathic pain, caused by a somatosensory nervous system lesion or disease, or nociplastic pain, which develops without evidence of somatosensory system damage. Since there is no gold standard for the diagnosis of pathological pain subtypes, the proper classification of individual patients is currently an unmet challenge for clinicians. While the determination of specific biomarkers for each condition by current biochemical techniques is a complex task, the use of multimolecular techniques, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), combined with artificial intelligence allows specific fingerprints for pathological pain-subtypes to be obtained, which may be useful for diagnosis. We analyzed whether the information provided by the mass spectra of serum samples of four experimental models of neuropathic and nociplastic pain combined with their functional pain outcomes could enable pathological pain subtype classification by artificial neural networks. As a result, a simple and innovative clinical decision support method has been developed that combines MALDI-TOF MS serum spectra and pain evaluation with its subsequent data analysis by artificial neural networks and allows the identification and classification of pathological pain subtypes in experimental models with a high level of specificity.
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Affiliation(s)
- Meritxell Deulofeu
- Research
Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department
of Medical Sciences, University of Girona, Girona, Catalonia 17003, Spain,Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5/A14, 625 00 Brno, Czech Republic,Department
of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Eladia M. Peña-Méndez
- Department
of Chemistry, Analytical Chemistry Division, Faculty of Sciences, University of La Laguna, 38204 San Cristóbal de
La Laguna, Tenerife, Spain
| | - Petr Vaňhara
- Department
of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Josef Havel
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5/A14, 625 00 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Lukáš Moráň
- Department
of Histology and Embryology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic,Research
Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 62500 Brno, Czech Republic
| | - Lukáš Pečinka
- Department
of Chemistry, Faculty of Science, Masaryk
University, Kamenice 5/A14, 625 00 Brno, Czech Republic,International
Clinical Research Center, St. Anne’s
University Hospital, 656
91 Brno, Czech Republic
| | - Anna Bagó-Mas
- Research
Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department
of Medical Sciences, University of Girona, Girona, Catalonia 17003, Spain
| | - Enrique Verdú
- Research
Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department
of Medical Sciences, University of Girona, Girona, Catalonia 17003, Spain
| | - Victoria Salvadó
- Department
of Chemistry, Faculty of Science, University
of Girona, 17071 Girona, Catalonia, Spain,
| | - Pere Boadas-Vaello
- Research
Group of Clinical Anatomy, Embryology and Neuroscience (NEOMA), Department
of Medical Sciences, University of Girona, Girona, Catalonia 17003, Spain,
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6
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He J, Liu O, Guo X. Deep Learning Based MS2 Feature Detection for Data-Independent Shotgun Proteomics. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE 2022; 2022:2342-2348. [PMID: 37635836 PMCID: PMC10457098 DOI: 10.1109/bibm55620.2022.9995258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Accuracy of peptide identification in LC-MS analysis is crucial for information regarding the aspects of proteins that aid in biomarker discovery and the profiling of complex proteomes. The detection of peptide fragment ions in tandem mass spectrometry is still challenging given that current tools were not created or tested for the low-abundance, low-peak fragments of peptides found in MS2 data. Feature detection, a crucial pre-processing step in the LC-MS analysis pipeline that quantifies peptides by their mass-to-charge ratio, retention time, and intensity, is particularly challenging due to the overlapping nature of peptides and weak signals that are often indistinguishable from noises, thus creating a reliance on rigid mathematical structures and heuristics. In this study, we developed a deep-learning-based model with an innovative sliding window process that enables high-resolution processing of quantitative MS/MS data to conduct MS2 feature detection. Experimental results show that our model can produce more accurate values and identifications than existing feature detection tools, as well as a high rate of true positive features quantified. Therefore, we believe that our model illustrates the advantages of deep learning techniques applied towards computational proteomics.
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Affiliation(s)
- Jonathan He
- Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA
| | - Olivia Liu
- Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA
| | - Xuan Guo
- Department of Computer Science and Engineering, Univeristy of North Texas, Denton, USA
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7
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Antimicrobial peptides from freshwater invertebrate species: potential for future applications. Mol Biol Rep 2022; 49:9797-9811. [PMID: 35716292 DOI: 10.1007/s11033-022-07483-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
Invertebrates are a significant source of antimicrobial peptides because they lack an adaptive immune system and must rely on their innate immunity to survive in a pathogen-infested environment. Various antimicrobial peptides that represent major components of invertebrate innate immunity have been described in a number of investigations over the last few decades. In freshwater invertebrates, antimicrobial peptides have been identified in arthropods, annelids, molluscs, crustaceans, and cnidarians. Freshwater invertebrate species contain antimicrobial peptides from the families astacidin, macin, defensin, and crustin, as well as other antimicrobial peptides that do not belong to these families. They show broad spectrum activities greatly directed against bacteria and to a less extent against fungi and viruses. This review focuses on antimicrobial peptides found in freshwater invertebrates, highlighting their features, structure-activity connections, antimicrobial processes, and possible applications in the food industry, animal husbandry, aquaculture, and medicine. The methods for their synthesis, purification, and characterization, as well as the obstacles and strategies for their development and application, are also discussed.
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8
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Mani DR, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA. Cancer proteogenomics: current impact and future prospects. Nat Rev Cancer 2022; 22:298-313. [PMID: 35236940 DOI: 10.1038/s41568-022-00446-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.
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Affiliation(s)
- D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
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9
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Zerfas BL, Trader DJ. Synthesis and Application of an Activity-Based Peptide-Peptoid Hybrid Probe for the Immunoproteasome. ACTA ACUST UNITED AC 2020; 11:e76. [PMID: 31860787 DOI: 10.1002/cpch.76] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The immunoproteasome (iCP), a specific isoform of the proteasome's catalytic particle, is becoming an important protein complex of interest in various diseases. However, there is still much left to be learned about its activity in cells and how this can be altered by various endogenous conditions or with treatment with small molecules. Current strategies to investigate the iCP lack in their ability to be used in live, intact cells, limiting them to use in endpoint experiments. The iCP-selective probe presented here has been shown to be compatible with various live-cell assays, including monitoring iCP activity kinetically in a plate reader-based assay and observing single cells with confocal microscopy. A well-studied iCP-selective inhibitor, ONX-0914, has also been demonstrated to decrease the fluorescence signal of the iCP probe in both of these assays, showing its potential function in investigating small-molecule modulators of the iCP. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of an immunoproteasome-selective peptide-peptoid hybrid probe Basic Protocol 2: Expression of the immunoproteasome in A549 cells Basic Protocol 3: Using the immunoproteasome probe to monitor activity in live cells with a fluorescence plate reader Basic Protocol 4: Using the immunoproteasome probe to monitor activity in live cells with confocal microscopy.
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Affiliation(s)
- Breanna L Zerfas
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana
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10
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Cautereels J, Van Hee N, Chatterjee S, Van Alsenoy C, Lemière F, Blockhuys F. QCMS 2 as a new method for providing insight into peptide fragmentation: The influence of the side-chain and inter-side-chain interactions. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4446. [PMID: 31652378 DOI: 10.1002/jms.4446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/12/2019] [Accepted: 09/21/2019] [Indexed: 06/10/2023]
Abstract
The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS2 ), which is based on quantum chemical calculations of bond orders, reaction, and transition-state energies at the DFT/B3LYP/6-311+G* level of theory. The method was used to describe the fragmentation pathways of five X-His-Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter-side-chain interactions on the fragmentation. The main features in the mass spectra of the five tripeptides were correctly reproduced, and a number of fragments were assigned to fragmentations involving the side chain and the influence of inter-side-chain interactions. Product ion spectra were recorded to evaluate the capabilities and limitations of QCMS2 and a number of conventional tools.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Nils Van Hee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Sneha Chatterjee
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | - Filip Lemière
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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11
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Cautereels J, Giribaldi J, Enjalbal C, Blockhuys F. Quantum chemical mass spectrometry: Ab initio study of b 2 -ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8778. [PMID: 32144813 DOI: 10.1002/rcm.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Both amide bond protonation triggering peptide fragmentations and the controversial b2 -ion structures have been subjects of intense research. The involvement of histidine (H), with its imidazole side chain that induces specific dissociation patterns involving inter-side-chain (ISC) interactions, in b2 -ion formation was investigated, focusing on the QHS model tripeptide. METHODS To identify the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b2 -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. Electrospray ionization ion trap mass spectrometry allowed the recording of MS2 and MS3 tandem mass spectra, whereas the Quantum Chemical Mass Spectrometry for Materials Science (QCMS2 ) method was used to predict fragmentation patterns. RESULTS Whereas it is very difficult to differentiate among protonated oxazolone, diketopiperazine, or lactam b2 -ions using MS2 and MS3 mass spectra, the calculations indicated that the QH b2 -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the formation of diketopiperazine less likely as it requires an additional step for its formation. CONCLUSIONS In contrast to glycine-histidine-containing b2 -ions, known to be issued from the backbone-imidazole cyclization, we found that interactions between the side chains were not obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.
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Affiliation(s)
- Julie Cautereels
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | | | | | - Frank Blockhuys
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
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12
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Messmer D, Sánchez-Ferrer A, Tacke S, Yu H, Nüsse H, Klingauf J, Wepf R, Kröger M, Halperin A, Mezzenga R, Schlüter AD. Can one determine the density of an individual synthetic macromolecule? SOFT MATTER 2019; 15:6547-6556. [PMID: 31359025 DOI: 10.1039/c9sm01220f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Dendronized polymers (DPs) are large and compact main-chain linear polymers with a cylindrical shape and cross-sectional diameters of up to ∼15 nm. They are therefore considered molecular objects, and it was of interest whether given their experimentally accessible, well-defined dimensions, the density of individual DPs could be determined. We present measurements on individual, deposited DP chains, providing molecular dimensions from scanning and transmission electron microscopy and mass-per-length values from quantitative scanning transmission electron microscopy. These results are compared with density values obtained from small-angle X-ray scattering on annealed bulk specimen and with classical envelope density measurements, obtained using hydrostatic weighing or a density gradient column. The samples investigated comprise a series of DPs with side groups of dendritic generations g = 1-8. The key findings are a very large spread of the density values over all samples and methods, and a consistent increase of densities with g over all methods. While this work highlights the advantages and limitations of the applied methods, it does not provide a conclusive answer to the question of which method(s) to use for the determination of densities of individual molecular objects. We are nevertheless confident that these first attempts to answer this challenging question will stimulate more research into this important aspect of polymer and soft matter science.
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Affiliation(s)
- Daniel Messmer
- Department of Materials, ETH Zürich, Polymer Chemistry & Polymer Physics, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
| | - Antoni Sánchez-Ferrer
- Department of Health Sciences and Technology, ETH Zürich, Laboratory of Food and Soft Materials, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - Sebastian Tacke
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Hao Yu
- Department of Materials, ETH Zürich, Polymer Chemistry & Polymer Physics, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
| | - Harald Nüsse
- Institute of Medial Physics and Biophysics, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
| | - Jürgen Klingauf
- Institute of Medial Physics and Biophysics, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
| | - Roger Wepf
- Institute of Medial Physics and Biophysics, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 31, 48149 Münster, Germany
| | - Martin Kröger
- Department of Materials, ETH Zürich, Polymer Chemistry & Polymer Physics, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
| | - Avraham Halperin
- Laboratoire de Spectrometrie Physique, CNRS University Joseph Fourier, BP 87, 38402 Saint Martin d'Hères cedex, France
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zürich, Laboratory of Food and Soft Materials, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
| | - A Dieter Schlüter
- Department of Materials, ETH Zürich, Polymer Chemistry & Polymer Physics, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
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13
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Pedro AQ, Queiroz JA, Passarinha LA. Smoothing membrane protein structure determination by initial upstream stage improvements. Appl Microbiol Biotechnol 2019; 103:5483-5500. [PMID: 31127356 PMCID: PMC7079970 DOI: 10.1007/s00253-019-09873-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
Abstract
Membrane proteins (MP) constitute 20–30% of all proteins encoded by the genome of various organisms and perform a wide range of essential biological functions. However, despite they represent the largest class of protein drug targets, a relatively small number high-resolution 3D structures have been obtained yet. Membrane protein biogenesis is more complex than that of the soluble proteins and its recombinant biosynthesis has been a major drawback, thus delaying their further structural characterization. Indeed, the major limitation in structure determination of MP is the low yield achieved in recombinant expression, usually coupled to low functionality, pinpointing the optimization target in recombinant MP research. Recently, the growing attention that have been dedicated to the upstream stage of MP bioprocesses allowed great advances, permitting the evolution of the number of MP solved structures. In this review, we analyse and discuss effective solutions and technical advances at the level of the upstream stage using prokaryotic and eukaryotic organisms foreseeing an increase in expression yields of correctly folded MP and that may facilitate the determination of their three-dimensional structure. A section on techniques used to protein quality control and further structure determination of MP is also included. Lastly, a critical assessment of major factors contributing for a good decision-making process related to the upstream stage of MP is presented.
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Affiliation(s)
- Augusto Quaresma Pedro
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
- CICECO - Aveiro Institute of Materials, Department of Chemistry, Universidade de Aveiro, 3810-193, Aveiro, Portugal
| | - João António Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal
| | - Luís António Passarinha
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
- UCIBIO@REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.
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14
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Tang HY, Speicher DW. Experimental Assignment of Disulfide-Bonds in Purified Proteins. ACTA ACUST UNITED AC 2019; 96:e86. [PMID: 30747488 DOI: 10.1002/cpps.86] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The formation of disulfide bonds in proteins is an important post-translational modification that is critical for stabilizing the native structures of proteins, particularly proteins exposed to oxidizing environments. For this reason, most cysteines in secreted proteins or protein domains on the surface of the cell are in disulfides, whereas most cysteines in the cytoplasm are in the unmodified -SH form. Disulfide linkages must be experimentally determined, as they cannot be predicted from amino acid sequence. These assignments provide insights into three-dimensional structure and contribute to the understanding of structural-functional relationships. This unit details a series of protocols that have been applied successfully to map disulfide bonds in proteins. The general strategy involves chemical or proteolytic cleavage of the protein followed by chromatographic separation of the resultant peptides. Mass spectrometry is used to identify disulfide-containing peptides and determine sites of disulfide linkage. A partial reduction and alkylation strategy for mapping disulfide linkages in peptides with multiple disulfide bonds is also presented. © 2019 by John Wiley & Sons, Inc.
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15
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Deng J, Erdjument-Bromage H, Neubert TA. Quantitative Comparison of Proteomes Using SILAC. ACTA ACUST UNITED AC 2018; 95:e74. [PMID: 30238645 DOI: 10.1002/cpps.74] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) has become very popular as a quantitative proteomic method since it was firstly introduced by Matthias Mann's group in 2002. It is a metabolic labeling strategy in which isotope-labeled amino acids are metabolically incorporated in vivo into proteins during translation. After natural (light) or heavy amino acid incorporation, differentially labeled samples are mixed immediately after cell lysis and before any further processing, which minimizes quantitative errors caused by handling different samples in parallel. In this unit, we describe protocols for basic duplex SILAC, triplex SILAC for use in nondividing cells such as neurons, and for measuring amounts of newly synthesized proteins. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jingjing Deng
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
| | - Hediye Erdjument-Bromage
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, New York
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16
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Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J. Genome annotation for clinical genomic diagnostics: strengths and weaknesses. Genome Med 2017; 9:49. [PMID: 28558813 PMCID: PMC5448149 DOI: 10.1186/s13073-017-0441-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial. Here, we discuss and illustrate the strengths and weaknesses of approaches for the annotation and classification of important elements of protein-coding genes, other genomic elements such as pseudogenes and the non-coding genome, comparative-genomic approaches for inferring gene function, and new technologies for aiding genome annotation, as a practical guide for clinicians when considering pathogenic sequence variation. Complete and accurate annotation of structure and function of genome features has the potential to reduce both false-negative (from missing annotation) and false-positive (from incorrect annotation) errors in causal variant identification in exome and genome sequences. Re-analysis of unsolved cases will be necessary as newer technology improves genome annotation, potentially improving the rate of diagnosis.
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Affiliation(s)
- Charles A Steward
- Congenica Ltd, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1DR, UK. .,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | | | - Berge A Minassian
- Department of Pediatrics (Neurology), University of Texas Southwestern, Dallas, TX, USA.,Program in Genetics and Genome Biology and Department of Paediatrics (Neurology), The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, WC1N 3BG, UK.,Chalfont Centre for Epilepsy, Chesham Lane, Chalfont St Peter, Buckinghamshire, SL9 0RJ, UK
| | - Adam Frankish
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer Harrow
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,Illumina Inc, Great Chesterford, Essex, CB10 1XL, UK
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17
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Sen KI, Hepler R, Nanda H. Detection and Measurement of Methionine Oxidation in Proteins. ACTA ACUST UNITED AC 2017; 87:14.16.1-14.16.11. [DOI: 10.1002/cpps.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Robert Hepler
- Janssen Research & Development LLC, Spring House Pennsylvania
| | - Hirsh Nanda
- Janssen Research & Development LLC, Spring House Pennsylvania
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18
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Mahmoodi MM, Rashidian M, Zhang Y, Distefano MD. Application of meta- and para-Phenylenediamine as Enhanced Oxime Ligation Catalysts for Protein Labeling, PEGylation, Immobilization, and Release. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2015; 79:15.4.1-15.4.28. [PMID: 25640893 PMCID: PMC4357315 DOI: 10.1002/0471140864.ps1504s79] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Meta- and para-phenylenediamines have recently been shown to catalyze oxime and hydrazone ligation reactions at rates much faster than aniline, a commonly used catalyst. Here, we demonstrate how these new catalysts can be used in a generally applicable procedure for fluorescent labeling, PEGylation, immobilization, and release of aldehyde- and ketone- functionalized proteins. The chemical orthogonality of phenylenediamine-catalyzed oxime ligation versus copper-catalyzed click reaction has also been harnessed for simultaneous dual labeling of bifunctional proteins containing both aldehyde and alkyne groups in high yield.
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Affiliation(s)
| | - Mohammad Rashidian
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Yi Zhang
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
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19
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Dobroff AS, Rangel R, Guzman-Roja L, Salmeron CC, Gelovani JG, Sidman RL, Bologa CG, Oprea TI, Brinker CJ, Pasqualini R, Arap W. Ligand-directed profiling of organelles with internalizing phage libraries. ACTA ACUST UNITED AC 2015; 79:30.4.1-30.4.30. [PMID: 25640897 DOI: 10.1002/0471140864.ps3004s79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phage display is a resourceful tool to, in an unbiased manner, discover and characterize functional protein-protein interactions, create vaccines, and engineer peptides, antibodies, and other proteins as targeted diagnostic and/or therapeutic agents. Recently, our group has developed a new class of internalizing phage (iPhage) for ligand-directed targeting of organelles and to identify molecular pathways within live cells. This unique technology is suitable for applications ranging from fundamental cell biology to drug development. This unit describes the methods for generating and screening the iPhage display system, and explains how to select and validate candidate internalizing homing peptide.
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Affiliation(s)
- Andrey S Dobroff
- Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,These authors contributed equally to this work
| | - Roberto Rangel
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas.,These authors contributed equally to this work
| | - Liliana Guzman-Roja
- Cancer Research Program, Houston Methodist Research Institute, Houston, Texas.,These authors contributed equally to this work
| | - Carolina C Salmeron
- Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Juri G Gelovani
- Department of Biomedical Engineering, Wayne State University, Detroit, Michigan
| | - Richard L Sidman
- Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Cristian G Bologa
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Tudor I Oprea
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - C Jeffrey Brinker
- Department of Chemical and Nuclear Engineering, The University of New Mexico Cancer Center, Albuquerque, New Mexico
| | - Renata Pasqualini
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,These authors contributed equally as senior authors to this work
| | - Wadih Arap
- Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, New Mexico.,These authors contributed equally as senior authors to this work
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20
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Raynal B, Lenormand P, Baron B, Hoos S, England P. Quality assessment and optimization of purified protein samples: why and how? Microb Cell Fact 2014; 13:180. [PMID: 25547134 PMCID: PMC4299812 DOI: 10.1186/s12934-014-0180-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/10/2014] [Indexed: 01/27/2023] Open
Abstract
Purified protein quality control is the final and critical check-point of any protein production process. Unfortunately, it is too often overlooked and performed hastily, resulting in irreproducible and misleading observations in downstream applications. In this review, we aim at proposing a simple-to-follow workflow based on an ensemble of widely available physico-chemical technologies, to assess sequentially the essential properties of any protein sample: purity and integrity, homogeneity and activity. Approaches are then suggested to optimize the homogeneity, time-stability and storage conditions of purified protein preparations, as well as methods to rapidly evaluate their reproducibility and lot-to-lot consistency.
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Affiliation(s)
- Bertrand Raynal
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Pascal Lenormand
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Bruno Baron
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Sylviane Hoos
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
| | - Patrick England
- Institut Pasteur, Biophysics of Macromolecules and their Interactions, 25 rue du Docteur Roux, 75724, Paris Cedex 15, France.
- CNRS-UMR3528, Institut Pasteur, Departement of Structural Biology and Chemistry, Paris, France.
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21
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Qiu X, Zhang H, Lai Y. Quantitative targeted proteomics for membrane transporter proteins: method and application. AAPS JOURNAL 2014; 16:714-26. [PMID: 24830943 DOI: 10.1208/s12248-014-9607-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/05/2014] [Indexed: 01/04/2023]
Abstract
Although global proteomics has shown promise for discovery of many new proteins, biomarkers, protein modifications, and polymorphisms, targeted proteomics is emerging in the proteomics research field as a complement to untargeted shotgun proteomics, particularly when a determined set of low-abundance functional proteins need to be measured. The function and expression of proteins related to drug absorption, distribution, metabolism, and excretion (ADME) such as cytochrome P450 enzymes and membrane transporters are of great interest in biopharmaceutical research. Since the variation in ADME-related protein expression is known to be a major complicating factor encountered during in vitro-in vivo and in vivo-in vivo extrapolations (IVIVE), the accurate quantification of the ADME proteins in complex biological systems becomes a fundamental element in establishing IVIVE for pharmacokinetic predictions. In this review, we provide an overview of relevant methodologies followed by a summary of recent applications encompassing mass spectrometry-based targeted quantifications of membrane transporters.
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Affiliation(s)
- Xi Qiu
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey, 08543, USA
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22
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Sokolowska I, Wetie AGN, Woods AG, Darie CC. Applications of Mass Spectrometry in Proteomics. Aust J Chem 2013. [DOI: 10.1071/ch13137] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).
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23
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Proteomic and scanning electron microscopic analysis of submandibular sialoliths. Clin Oral Investig 2012; 17:1709-17. [PMID: 23103960 DOI: 10.1007/s00784-012-0870-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/17/2012] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Several theories have been proposed regarding the genesis of sialoliths, including the organic core theory, which suggests epithelial or bacterial etiology originating in the central core. Our aim was to use novel methodologies to analyze central areas (the core) of calculi from sialolithiasis patients. MATERIALS AND METHODS The structures of the halves of six submandibular salivary stones were analyzed by scanning electron microscopy (SEM). After structural analysis, from the other six halves, samples from the central parts of the core and peripheral parts of the core were digested with trypsin and analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry. The peptide mass fingerprints were compared with the results of in silico digestion. RESULTS SEM analysis of the sialoliths showed that organic structures (collagen/fibrous-like structures, bacterial fragments) were visible only outside of the core in the concentric layers of external areas, but not in the core area. The mass spectrometry (MS)/MS post-source decay experiments were completed from the four, most intense signals observed in the MS spectrum and human defensin was proven to be present in three of the examined samples, originated from the peripheral region of three cores. CONCLUSIONS Although proteomic analysis demonstrated defensin protein in the peripheral region of the core in three sialoliths, SEM failed to prove organic structures in the core. CLINICAL RELEVANCE New investigation modalities still cannot prove organic structures in the core, henceforward challenging the organic core theory.
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24
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Darie CC, Deinhardt K, Zhang G, Cardasis HS, Chao MV, Neubert TA. Identifying transient protein-protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry. Proteomics 2011; 11:4514-28. [PMID: 21932443 DOI: 10.1002/pmic.201000819] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 08/23/2011] [Accepted: 08/31/2011] [Indexed: 11/11/2022]
Abstract
Receptor tyrosine kinases (RTKs) are proteins that upon ligand stimulation undergo dimerization and autophosphorylation. Eph receptors (EphRs) are RTKs that are found in different cell types, from both tissues that are developing and from mature tissues, and play important roles in the development of the central nervous system and peripheral nervous system. EphRs also play roles in synapse formation, neural crest formation, angiogenesis and in remodeling the vascular system. Interaction of EphRs with their ephrin ligands lead to activation of signal transduction pathways and formation of many transient protein-protein interactions that ultimately leads to cytoskeletal remodeling. However, the sequence of events at the molecular level is not well understood. We used blue native PAGE and MS to analyze the transient protein-protein interactions that resulted from the stimulation of EphB2 receptors by their ephrinB1-Fc ligands. We analyzed the phosphotyrosine-containing protein complexes immunoprecipitated from the cell lysates of both unstimulated (-) and ephrinB1-Fc-stimulated (+) NG108 cells. Our experiments allowed us to identify many signaling proteins, either known to be part of EphB2 signaling or new for this pathway, which are involved in transient protein-protein interactions upon ephrinB1-Fc stimulation. These data led us to investigate the roles of proteins such as FAK, WAVEs and Nischarin in EphB2 signaling.
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Affiliation(s)
- Costel C Darie
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York, NY, USA.
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