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Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Related Experiment Video

Updated: May 7, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations

Published on: April 26, 2024

RNA structure experimental analysis--chemical modification.

Zhili Xu¹, Gloria Culver

¹Department of Biology, University of Rochester, Rochester, NY, USA.

Methods in Enzymology

|September 17, 2013

Summary

This summary is machine-generated.

This protocol identifies protein footprints on RNA and analyzes RNA secondary structure. It is optimized for large RNA molecules but adaptable for small RNAs, aiding in molecular biology research.

Keywords:

Dimethyl sulfate (DMS)Primer extension Quantification and normalization RNA RNA extraction RNA structure experimental analysis Ribonucleoprotein (RNP)

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Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Proteins interact with RNA molecules in various cellular processes.
Understanding these interactions is crucial for deciphering gene regulation and function.
Analyzing RNA secondary structure provides insights into its stability and interactions.

Purpose of the Study:

To present a protocol for identifying protein footprints on RNA.
To demonstrate the protocol's utility in analyzing RNA secondary structure.
To highlight the protocol's adaptability for different RNA sizes.

Main Methods:

The protocol involves specific steps to detect protein binding sites on RNA.
Techniques are employed to map the RNA regions protected by protein binding.
Methods are included for analyzing the resulting RNA secondary structures.

Main Results:

The protocol successfully identifies 'footprints' of protein binding on RNA molecules.
The method allows for detailed analysis of RNA secondary structure.
The protocol is effective for large RNA molecules and can be modified for small RNAs.

Conclusions:

This protocol offers a robust method for studying protein-RNA interactions.
It provides a valuable tool for RNA structure and function analysis.
The protocol's versatility makes it applicable across a range of RNA research areas.