Practical conversion from torsion space to Cartesian space for in silico protein synthesis
Jerod Parsons1, J Bradley Holmes, J Maurice Rojas
1Texas Agricultural Experiment Station, Texas A&M University, College Station, Texas 77843, USA.
Journal of Computational Chemistry
|May 18, 2005
Summary
A new method called the Natural Extension Reference Frame (NeRF) efficiently converts molecular structural data into precise atomic coordinates. This computational approach is faster and more stable than existing techniques for modeling proteins and DNA.
Area of Science:
- Computational chemistry
- Structural biology
- Robotics
Background:
- Translating bond angles and lengths to Cartesian coordinates is crucial for molecular modeling.
- Existing methods are computationally intensive and can lack numerical stability.
Purpose of the Study:
- To compare five established methods for protein backbone extension.
- To introduce and evaluate the Natural Extension Reference Frame (NeRF) algorithm.
Main Methods:
- Serial chain extension from bond angles and lengths.
- Comparison of algorithms based on operations, speed, stability, and parallelization.
- Implementation and benchmarking of the NeRF method.
Main Results:
- The NeRF algorithm requires 47% fewer floating point operations compared to traditional methods.
- NeRF demonstrates superior intrinsic numerical stability.
- NeRF offers potential for parallel processor acceleration.
Conclusions:
- The NeRF method is a more efficient and stable algorithm for converting structural data to atomic coordinates.
- NeRF's unique factorization may represent a minimal operation set for chain extension.
- This advancement benefits protein, DNA, and polymer modeling, as well as robotics.
Related Concept Videos
01:44Termination 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...
01:34Directing Proteins to the Rough Endoplasmic Reticulum
The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
01:20Cotranslational Protein Translocation
Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
01:26Cartesian Form for Vector Formulation
The Cartesian form for vector formulation is a process to calculate the moment of force using the position and force vectors. The moment of force is defined as the cross-product of these vectors, making it a vector quantity. The Cartesian form of the position and force vectors involves unit vectors, which can be used to express the cross-product in determinant form.
01:16Torsion of Noncircular Members
Circular shafts undergoing torsional stress maintain their cross-sectional integrity due to their axisymmetric nature. This symmetry ensures an even distribution of stress, allowing the shaft to withstand torsion without distorting. In contrast, square bars, lacking this axial symmetry, experience significant distortion across their cross-sections when subjected to torsion, with the exception of along their diagonals and at lines connecting midpoints. A detailed examination of a cubic element...
01:20Torsion in Vector Calculus
A toy train ascending a winding track that curves and tilts offers an intuitive view of torsion, a key geometric concept in the study of space curves. While curvature measures how sharply a path bends, torsion captures how the path twists out of the plane of bending. This twisting behavior is crucial in understanding three-dimensional motion and is precisely described using the Frenet–Serret framework.At each point along a space curve, the Frenet–Serret frame consists of three orthogonal unit...