Related Experiment Video
Updated: Apr 6, 2026
22:27
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
412.4K
Fractal Dimensions of Macromolecular Structures
Nickolay Todoroff1, Jens Kunze1, Herman Schreuder2
1Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland fax: (+41) 44 633 13 79.
Molecular Informatics
|July 28, 2015
Summary
Molecular surface roughness, measured by fractal dimension (D), correlates with ligand binding potential in macromolecules. This suggests more of a protein
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Understanding macromolecule function requires quantifying their properties.
- Molecular surface irregularity, or roughness, is a geometric feature measurable by fractal dimension (D).
Purpose of the Study:
- To investigate the correlation between macromolecular surface roughness and ligand binding potential.
- To quantify surface roughness across a large set of biological macromolecules.
Main Methods:
- Quantified fractal dimension (D) to measure surface roughness of macromolecules.
- Surveyed a large dataset of biological macromolecules.
Main Results:
- Macromolecular surface roughness (D values between 2.0 and 2.4) correlates with ligand binding potential.
- Surface areas involved in molecular interactions (e.g., ligand-binding pockets) show higher local fractal dimension fluctuations.
- Approximately 22% of protein surface area outside known binding sites may be ligandable.
Conclusions:
- Macromolecular surface roughness is a key factor in ligand binding.
- Findings offer new insights into macromolecular structure and have implications for drug design and systems biology.
Related Concept Videos
02:18X-ray Crystallography
26.9K
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...
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...
26.9K
01:29Determination of Crystal Structures
111
In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
111
01:18Molecular Shapes
63.4K
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...
63.4K
02:22Structures of Solids
21.9K
Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...
21.9K
02:00Molecular Models
45.6K
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.
45.6K