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Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Termination of Translation01:44

Termination of Translation

The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...

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Related Experiment Video

Updated: Jun 22, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
09:15

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Exploring ribozyme conformational changes with X-ray crystallography.

Robert C Spitale1, Joseph E Wedekind

  • 1Department of Chemistry, Biological Chemistry Cluster, Rochester, NY 14627-0216, USA.

Methods (San Diego, Calif.)
|June 30, 2009
PubMed
Summary
This summary is machine-generated.

Understanding RNA structure and dynamics is key to RNA biology. This study uses X-ray crystallography and computational methods to explore RNA conformational changes, providing insights into molecular motion and function.

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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

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Last Updated: Jun 22, 2026

Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

Published on: January 10, 2018

Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050
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X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050

Published on: May 13, 2020

Area of Science:

  • RNA structural biology
  • Biophysics
  • Biochemistry

Background:

  • Relating three-dimensional RNA structure to biological function is a central challenge.
  • X-ray crystallography and NMR spectroscopy are key techniques for RNA structure determination.
  • NMR spectroscopy excels at probing RNA dynamics and molecular motion.

Purpose of the Study:

  • To describe techniques for exploring conformational changes in RNA molecules.
  • To provide insights into global and local molecular motion relevant to biological function.
  • To demonstrate methods applicable to RNA systems, using the hairpin ribozyme as a model.

Main Methods:

  • Utilizing X-ray crystallography for high-resolution RNA structure determination.
  • Employing NMR spectroscopy to investigate RNA dynamics and molecular motion.
  • Developing and applying computational approaches to analyze structural ensembles and conformational changes.

Main Results:

  • X-ray crystallography, despite limitations in dynamics, provides substantial RNA structural information.
  • Advancements in computing and synchrotron sources accelerate RNA crystal structure determination.
  • Ensemble analysis from multiple crystal structures reveals insights into RNA molecular motion.

Conclusions:

  • Techniques involving construct design, recognition of long-range changes, and single-element modifications can explore RNA conformational dynamics.
  • These methods, applied to the hairpin ribozyme, offer a framework for studying other RNA systems.
  • Integrating structural and dynamic information is crucial for understanding RNA function.