Integrated Methods in Protein Biochemistry. Part C / edited by Arun K. Shukla.

Format:

Book

Contributor:

Shukla, Arun K., editor.

Series:

Methods in enzymology ; Volume 682.

Methods in enzymology ; Volume 682

Language:

English

Subjects (All):

Biochemistry.

Proteins--Analysis.

Proteins.

Proteomics--Methodology.

Proteomics.

Physical Description:

1 online resource (496 pages)

Place of Publication:

Cambridge, MA : Academic Press, [2023]

Summary:

Integrated Methods in Protein Biochemistry: Part B, Volume 678 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of topics, including Precise modification of native proteins, purification, and analysis of bioconjugates, NanoBiT-based methods to monitor the activation and modulation of RTKs, The interplay of G-protein ß? subunit and PLC-ß enzyme in PIP2 hydrolysis and downstream signaling, Structure and function of bacterial secretion system, Tools and protocols for probing protein sumoylation, Spectroscopic analysis of cysteine dioxygenase: a mammalian thiol-dioxygenase, DeGlyPHER: MS-based analysis of viral spike N-glycoforms, and more. Additional sections cover Covalent protein painting: MS-based protein footprinting, Characterization of GPCR signaling complexes using negative-staining electron microscopy, Probing protein misfolding and dissociation with free electron laser, Optimized protocol for the characterization of Cas12a activities, Proximity proteomics for the identification and characterization of extracellular vesicles, Structural and Functional characterization of lytic polysaccharide monooxygenases, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in Methods in Enzymology series Includes the latest information on Integrated Methods in Protein Biochemistry.

Contents:

Intro

Integrated Methods in Protein Biochemistry: Part C

Copyright

Contents

Contributors

Preface

Chapter One: Nanoluciferase-based complementation assays to monitor activation, modulation and signaling of receptor tyro ...

1. Introduction

2. Before you begin

3. Materials and equipment

3.1. Cell culture and transfection

3.2. Sample preparation and reading for NLuc complementation assay

3.3. Sequences of NanoBiT tagged protein partners

3.3.1. RTK-SmBiT and RTK-LgBiT (dimerization assay)

3.3.2. RTK-LgBiT and Grb2-SmBiT or SmBiT-Cbl (recruitment assay)

4. Step-by-step method details

4.1. Cell preparation and transfection

4.1.1. Notes

4.2. Dimerization or adaptor/signaling protein recruitment assay performance and reading

4.2.1. Notes

4.3. Optional steps

5. Expected outcome and quantification

6. Advantages

7. Limitations

8. Alternative methods/procedures

Acknowledgments

References

Chapter Two: Molecular regulation of PLCβ signaling

2. Structure of PLC

3. Isoforms and splice variants of PLC

3.1. PLCβ

3.2. PLCγ

3.3. PLCδ

3.4. PLC

3.5. PLCzeta

3.6. PLCη

4. Physiological and pathological role of PLC-mediated signaling

4.1. Hematopoiesis and immune functions

4.2. Cell cycle

4.3. Brain and neuronal functions

4.4. Cancer

5. PLCβ activation and regulation

5.1. Gαq-mediated regulation of PLCβ

5.2. Gβγ: Governed PLCβ signaling regulation

5.3. Gβγ interacting regions of PLCβ

5.3.1. N terminal pleckstrin homology (PH) domain

5.3.2. Conserved helix in the Ct of the TIM barrel

6. Synergistic activation of PLCβ by Gαq and Gβγ

7. Modulation of Gαq and Gβγ-governed PLCβ signaling

8. Cell-tissue-organ specific expression profiles of Gβγ and PLCβ

9. Conclusions

Author contributions.

Funding information

Conflict of interests

Chapter Three: Laminar flow-based microfluidic systems for molecular interaction analysis-Part 1: Chip development, syste ...

2. Microfluidic device development

2.1. Device material and fabrication

2.2. Custom PDMS device design

2.3. Channel aspect ratio

2.4. Limitations of custom PDMS devices

2.5. Post-fabrication treatment to prevent adsorption

3. Fluidic actuation

3.1. Choosing a suitable flow rate

3.2. Controlling and measuring the flow rate

3.3. On-chip fluid reservoirs

4. Fluorescence detection

4.1. Fluorescent labelling of proteins for analysis in the LaMInA system

4.1.1. Fluorescein isothiocyanate (FITC)

4.1.2. FITC labelling of DHDPS

4.1.3. FITC labelling of rubisco

4.1.4. FITC-labelling of protein size standards

4.2. Alternative fluorescent dyes

4.2.1. Ortho-phthalaldehyde

4.2.2. Fluorescamine

4.3. Technical considerations for the fluorescence detection hardware

4.3.1. Colour charged-coupled device (CCD) camera

4.3.2. Monochromatic scientific complementary metal oxide semiconductor (CMOS) camera

4.3.3. Photomultiplier tube with CLS microscopy

5. Summary and conclusions

Chapter Four: Spectroscopic analysis of the mammalian enzyme cysteine dioxygenase

2. Spectroscopic analysis of CDO

2.1. Resting state ferrous enzyme

2.2. Substrate (analogue) bound CDO

2.3. Substrate (analogue) bound CDO incubated with superoxide surrogates

2.4. Secondary sphere CDO variants

Chapter Five: DeGlyPHER: Highly sensitive site-specific analysis of N-linked glycans on proteins

1.1. N-glycosylated viral spike proteins as vaccine candidates

1.2. Site-specific N-glycosylation analysis using HIV Env.

1.3. Breaking the sensitivity barrier using a ``single-pot´´ proteomic analysis

1.3.1. Proteinase K

1.3.2. Optimizing the reaction

1.4. Sequential deglycosylation

2.1. Buffer exchange and concentrating the sample

2.1.1. Buffer exchange

2.1.2. Freezing

2.1.3. Freeze-drying

2.2. Preparing reaction solutions

2.2.1. Solution X (for Endo H and Proteinase K).

2.2.2. Solution Y (for PNGase F)

2.3. Preparing proteinase K stock solution

3. Key resources table

4. Materials and equipment

5. Step-by-step method details

5.1. Reducing disulfide bridge(s)

5.2. Endo H treatment at protein level

5.3. Proteinase K digestion

5.4. Endo H treatment at peptide level

5.5. Freeze-drying the reaction and PNGase F treatment

5.6. LC-MS/MS

5.6.1. Q exactive HF-X with EASY-nLC 1200

5.6.2. timsTOF Pro with Evosep One

5.7. Data processing

6. Quantification and statistical analysis

6.1. Label-free quantitation

6.2. Data analysis using GlycoMSQuant

7. Expected outcomes

8. Advantages

9. Limitations

10. Optimization and troubleshooting

10.1. Validating efficiency of glycosidases

10.2. Comparing PK vs trypsin

10.3. DeGlyPHER vs our previous approach

10.4. Analyzing DeGlyPHER´s limit of sensitivity

10.5. Troubleshooting

11. Safety considerations and standards

12. Alternative methods/procedures

Chapter Six: Sample preparation for structural mass spectrometry via polyacrylamide gel electrophoresis

2. Sample preparation for top-down mass spectrometry by PEPPI-MS

2.1. Equipment

2.2. Reagents

2.3. Procedure

2.4. Notes

3. Sample preparation for native mass spectrometry by PEPPI-MS

3.1. Equipment

3.2. Reagent

3.3. Procedure

3.4. Notes.

4. Sample preparation for cross-linking mass spectrometry by PEPPI-AnExSP

4.1. Equipment

4.2. Reagents

4.3. Procedure

4.4. Notes

Chapter Seven: High-throughput screening of glycosynthases using azido sugars for oligosaccharides synthesis

2. Screening using cyn regulon based azide detection method

2.1. Summary

2.2. Preparation of error-prone PCR library

2.2.1. Materials and equipment

2.2.2. Procedure

2.2.3. Notes

2.3. Procedure for medium-throughput screening of mutants

2.3.1. Materials and equipment

2.3.2. Procedure

2.3.3. Notes

3. Screening using click chemistry based azide detection method

3.1. Summary

3.2. Preparation of error prone PCR library

3.2.1. Materials and equipment

3.2.2. Procedure

3.2.3. Notes

3.3. Procedure for high-throughput screening of mutants

3.3.1. Materials and equipment

3.3.2. Procedure

3.4. Notes

4. Summary and conclusions

Chapter Eight: Rational design, production and in vitro analysis of photoxenoproteins

2. Rational design of photoxenoproteins

3. Synthesis of phenylalanine-4-azobenzene AzoF

3.2. Reagents

4. Heterologous gene expression and purification of photoxenoproteins

5. Characterization of photoxenoproteins

5.1. Photochemical characterization of ONBY-containing POIs

5.2. Photophysical characterization of AzoF-containing POIs

5.2.1. Equipment

5.2.2. Reagents

5.2.3. Procedure

6. Evaluation of photocontrol

6.1. Photocontrol under steady-state conditions

6.2. Photocontrol during turnover

6.3. Example 1: Photocontrol of tryptophan synthase with ONBY

6.4. Example 2: Photocontrol of imidazole glycerol phosphate synthase with AzoF.

7. Notes

Chapter Nine: Chemical and structural approaches to investigate PTEN function and regulation

2. Biochemical assays to determine the conformational state of PTEN

3. Structural basis for N-terminal function and regulation

3.1. Production of semi-synthetic PTENs for protein X-ray crystallography

3.2. X-ray crystal structure of PTEN revealing N-terminal segment of PTEN

3.3. Production of semi-synthetic N-terminally labeled PTEN for macromolecular NMR

4. Structural basis for regulation of PTEN by C-terminal phosphorylation

4.1. Production of VSP for macromolecular NMR experiments

4.1.1. Isotopically labeling VSP for NMR assignments

4.1.2. Protein semi-synthesis to generate segmentally labeled phosphorylated VSP for macromolecular NMR

4.2. Structural model for how the C-terminal tail engages VSP

5. Summary and future directions

Chapter Ten: Analyzing protein posttranslational modifications using enzyme-catalyzed expressed protein ligation

2. General methods and statistical analysis

3. Purification of subtiligase

3.1. Materials and reagents

3.1.1. For expression and purification

3.2. Equipment

3.3.1. Transformation

3.3.2. Expression and purification

4. Synthesis of peptide using solid phase peptide synthesis (SPPS)

4.3. Procedure (8-10h)

5. Generation of POI C-terminal thioester

5.1. Materials and reagents

5.1.1. For expression and purification

5.2. Equipment

5.3. Procedure

5.3.1. Expression and purification of POI-MxeIntein-CBD fusion protein

5.3.2. Intein cleavage

5.4. Notes

6. Enzyme-catalyzed EPL, and affinity purification of protein ligation product using biotin tag.

6.1. Materials and reagents.

Notes:

Includes bibliographical references.

Description based on print version record.

Other Format:

Print version: Shukla, Arun K. Integrated Methods in Protein Biochemistry: Part C

ISBN:

9780443185939

OCLC:

1373987689