Related Experiment Video
Updated: Dec 6, 2025
12:38
Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction
Published on: August 9, 2011
17.7K
Helical ensembles outperform ideal helices in molecular replacement
Filomeno Sánchez Rodríguez1, Adam J Simpkin1, Owen R Davies2
1Institute of Structural, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom.
Acta Crystallographica. Section D, Structural Biology
|October 6, 2020
Summary
This study introduces novel helical ensembles for molecular replacement, improving protein structure solution rates by 30% and reducing computation time. This advance aids researchers when related protein structures are unavailable.
Area of Science:
- Structural biology
- Computational biology
- Biophysics
Background:
- Molecular replacement (MR) typically relies on known related structures as search models.
- Scarcity of known structures for novel protein families limits conventional MR.
- Existing methods like AMPLE (Automated Molecular Replacement using Libraries of Ensembles) have used ideal helical fragments.
Purpose of the Study:
- To explore the performance of libraries of helical ensembles generated by clustering helical segments for molecular replacement.
- To investigate the impact of B-factor treatments and structural heterogeneity on MR.
- To enhance the efficiency and success rate of the AMPLE software.
Main Methods:
- Generation of helical ensembles by clustering helical segments from protein structures.
- Testing these ensembles as search models in the AMPLE software.
- Evaluation of performance across different protein fold classes (transmembrane, globular, coiled-coil).
- Analysis of B-factor treatments and structural heterogeneity effects.
Main Results:
- A 30% increase in the number of solutions obtained using helical ensembles compared to ideal helices.
- Significant performance improvements observed across transmembrane, globular, and coiled-coil protein structures.
- Reduced computation time for AMPLE to achieve solutions with the new ensembles.
Conclusions:
- Helical ensembles represent a more effective search model library for molecular replacement than ideal helices.
- This enhancement broadens the applicability of AMPLE to a wider range of protein structures.
- Activating the 'helical ensembles' mode in AMPLE is recommended for improved structure determination.
Related Concept Videos
00:55DNA Helicases
23.5K
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
23.5K
02:06Newman Projections
19.8K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
19.8K
01:18Molecular Shapes
60.7K
Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
Two regions of electron density in a diatomic...
60.7K
02:00Molecular Models
43.0K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
43.0K
02:18Fischer Projections
15.7K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
15.7K
02:11Conformations of Cyclohexane
14.7K
Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal...
14.7K