scholarly journals The Fastest Simulation of Protein Folding Based on Torsion Angles

2020 ◽  
Author(s):  
Seonghoon Jeong
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Potential Energy ◽  
Torsion Angle ◽  
Stable State ◽  
Protein Backbone ◽  
Torsion Angles ◽  
Backbone Torsion Angle ◽  
Torsional Inertia ◽  
And Function

Abstract Backgrounds: Enormous number of possible conformations in the protein structure simulation have led molecular dynamics researchers to be frustrated until now. Some methods with defects ended their experiments into failure. This made them fail to determine the structure and function of folded protein in stable state with the lowest potential energy. This apparently exist in nature. The purpose of resolving a protein folding pathway that follows protein backbone residues torsional inertia was accomplished. Results A new method, torsion angle modeling, was adopted focused on the rotation of dihedral angles. The potential energy was calculated by rotating torsion angles of the peptide with 8 residues. It was found that when moving in the order of torsional inertia, 8 residues swivel in sequence. Six passes were repeated to find the lowest value. Conclusion The protein backbone torsion angle plays very important role in predicting protein structure. Actually it was thousand times faster or more than others to get the obvious pathway.

Molecular Origins of the Unique Conformational Properties of the Polysilanes: A Molecular Dynamics Study of Poly(Di-N-Hexylsilane)

1992 ◽  
Vol 278 ◽  
Author(s):  
William J. Welsh ◽  
Samuel H. Tersigni ◽  
Wangkan Lin
Keyword(s):  
Molecular Dynamics ◽  
Torsion Angle ◽  
Model Compound ◽  
Energy Surface ◽  
Conformational Dynamics ◽  
Conformational Transitions ◽  
Torsion Angles ◽  
Global Energy Minimum ◽  
Conformational Properties ◽  
Backbone Torsion Angle

AbstractThe conformational dynamics of a model compound for poly(di-n-hexylsilane) (PDHS) has been explored using the new molecular dynamics program MM3-MD. MM3-MD trajectories at variable temperatures reveal two abrupt conformational transitions, one near -182°C and another near -175°C, associated with two energy barriers on the potential-energy surface. The first transition near -182°C allows shifts in the backbone torsion angle from that defined by the global energy minimum designated off-trans to that corresponding to a statistical collection of torsion angles within the range trans ±30°. The second transition near -175°C allows the backbone torsion angle to explore the remainder of its torsional space. The sidechain dynamics follows a similar pattern. We suggest that the abrupt transition calculated here at -182°C for “gas.phase” PDHS corresponds to that observed for PDHS at -28°C in solution and at 42°C in the solid state.

scholarly journals Change in backbone torsion angle distribution on protein folding

2000 ◽  
Vol 9 (6) ◽  
pp. 1129-1136 ◽  
Author(s):  
Andrei-José Petrescu ◽  
Patrick Calmettes ◽  
Dominique Durand ◽  
Veronique Receveur ◽  
Jeremy C. Smith
Keyword(s):  
Protein Folding ◽  
Torsion Angle ◽  
Angle Distribution ◽  
Backbone Torsion Angle

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

The T3 Method (“T3 It!”): Transcribe → Translate → Transform

2017 ◽  
Vol 79 (4) ◽  
pp. 257-271
Author(s):  
Brett Malas
Keyword(s):  
Protein Folding ◽  
Protein Structure ◽  
Differentiated Instruction ◽  
Genetic Information ◽  
Structural Models ◽  
Structure And Function ◽  
Protein Structure And Function ◽  
Learning Contexts ◽  
Wide Range ◽  
And Function

Traditional transcription-translation exercises are instructionally incomplete by failing to link prescriptive genetic information with protein structure and function. The T3 Method solves this problem by adding a conceptually powerful yet easily learned third step where students use simple protein folding codes to transform their translations into corresponding protein structural models. This brings structural sense to sequence and makes the information-to-proteins connection that is so profoundly important to understand in biology more directly evident, experiential, and intrinsically meaningful. The T3 Method has further utility, proving versatile and adaptive to a wide range of academic levels and learning contexts, with possibilities for differentiated instruction, application, and extension.

scholarly journals TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e30361 ◽  
Author(s):  
Jiangning Song ◽  
Hao Tan ◽  
Mingjun Wang ◽  
Geoffrey I. Webb ◽  
Tatsuya Akutsu
Keyword(s):  
Support Vector Regression ◽  
Torsion Angle ◽  
Support Vector ◽  
Protein Backbone ◽  
Regression Approach ◽  
Backbone Torsion Angle

scholarly journals GlyConnect: a glycan-based conjugation extension of the GlycoDelete technology

2021 ◽  
Author(s):  
Wander Van Breedam ◽  
Karel Thooft ◽  
Francis Santens ◽  
Sandrine Vanmarcke ◽  
Elise Wyseure ◽  
...  
Keyword(s):  
Protein Structure ◽  
Structure And Function ◽  
Protein Backbone ◽  
Protein Structure And Function ◽  
Site Specific ◽  
And Function

Recently, our lab developed GlycoDelete, a technology suite that allows a radical simplification of eukaryotic N-glycosylation. The technology allows to produce glycoproteins that carry single GlcNAc, LacNAc, or LacNAc-Sia type glycans on their N-linked glycosylation sequons. GlycoDelete-type N-glycans are uniquely suited for glycan-based conjugation purposes, as these provide a short, homogeneous and hydrophilic link to the protein backbone. Targeting GlycoDelete-glycans allows for highly site-specific conjugation at sites in the protein which are normally occupied by bulky glycans, thus ensuring minimal interference with protein structure and function. The current manuscript describes the evaluation and optimization of both chemical and chemo-enzymatic conjugation of molecules onto the GlycoDelete-type glycans of a limited set of benchmark proteins

Sign in / Sign up

Export Citation Format

Share Document