SEQUENCE DESIGN AND FOLDING DYNAMICS OF LATTICE PROTEIN-LIKE MODELS

2002 ◽  
Vol 16 (04) ◽  
pp. 631-637 ◽  
Author(s):  
MENG QIN ◽  
JUN WANG ◽  
TANPING LI ◽  
WEI WANG
Keyword(s):  
Great Improvement ◽  
Design Method ◽  
Protein Sequences ◽  
Target Structure ◽  
Dynamic Features ◽  
Sequence Design ◽  
Model Protein ◽  
Folding Dynamics

A sequence design method based on maximizing the thermodynamic occupying probability of the target structure is investigated. Some model-protein sequences are designed using the occupying-probability-maximized procedure on a 3×3×3 lattice. The thermodynamic and dynamic features of these sequences show their great improvement comparing with those of the sequences designed by an energy-minimized method. A better foldability is achieved for the occupying-probability-maximized sequences. These results suggest that the native occupying probability rather than the energy would be a better judgment for protein-like models.

scholarly journals Learning protein constitutive motifs from sequence data

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jérôme Tubiana ◽  
Simona Cocco ◽  
Rémi Monasson
Keyword(s):  
Sequence Data ◽  
Protein Sequences ◽  
Sequence Information ◽  
Ligand Specificity ◽  
Protein Families ◽  
Restricted Boltzmann Machines ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Model Protein ◽  
Lattice Proteins

Statistical analysis of evolutionary-related protein sequences provides information about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their statistical features, can efficiently model protein families from sequence information. We here apply RBM to 20 protein families, and present detailed results for two short protein domains (Kunitz and WW), one long chaperone protein (Hsp70), and synthetic lattice proteins for benchmarking. The features inferred by the RBM are biologically interpretable: they are related to structure (residue-residue tertiary contacts, extended secondary motifs (α-helixes and β-sheets) and intrinsically disordered regions), to function (activity and ligand specificity), or to phylogenetic identity. In addition, we use RBM to design new protein sequences with putative properties by composing and 'turning up' or 'turning down' the different modes at will. Our work therefore shows that RBM are versatile and practical tools that can be used to unveil and exploit the genotype–phenotype relationship for protein families.

Research and Realization of the Control Performance in the Electro-Magnetic Gears Transmission System

2013 ◽  
Vol 341-342 ◽  
pp. 1071-1075
Author(s):  
Jian Na Huang ◽  
Yan Ma
Keyword(s):  
Electric Current ◽  
Design Method ◽  
Transmission System ◽  
Dynamic Features ◽  
The Neural Network ◽  
Gear Transmission System ◽  
Magnetic Gear ◽  
Time Basis ◽  
Electro Magnetic ◽  
Set Up

This paper has set up the dynamic model of the electro-magnetic gear and deduced the transfer function which the input is electric current and the output is torque, and designed the neural network PID controller in the electro-magnetic gears control system according to the principle of the electro-magnetic gear transmission system, which has been simulated dynamically under MATLAB environment. The result shows that design method can adjust changes in real-time basis according to the input electric current, which improves the dynamic features greatly and achieves steady output of the system.

scholarly journals A simple and effective assembly sequence design method

2021 ◽  
Vol 1983 (1) ◽  
pp. 012102
Author(s):  
Chao Shao ◽  
Yuanzi Zhou ◽  
Qiang Zhang ◽  
Yuhang Tang ◽  
Jun Jiang
Keyword(s):  
Design Method ◽  
Assembly Sequence ◽  
Sequence Design

Increasing the efficiency and accuracy of the ABACUS protein sequence design method

2019 ◽  
Vol 36 (1) ◽  
pp. 136-144 ◽  
Author(s):  
Peng Xiong ◽  
Xiuhong Hu ◽  
Bin Huang ◽  
Jiahai Zhang ◽  
Quan Chen ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Design Method ◽  
Solvent Accessibility ◽  
Supplementary Information ◽  
Survey Method ◽  
Energy Functions ◽  
Sequence Design ◽  
Feature Spaces ◽  
Empirical Function ◽  
Representative Points

Abstract Motivation The ABACUS (a backbone-based amino acid usage survey) method uses unique statistical energy functions to carry out protein sequence design. Although some of its results have been experimentally verified, its accuracy remains improvable because several important components of the method have not been specifically optimized for sequence design or in contexts of other parts of the method. The computational efficiency also needs to be improved to support interactive online applications or the consideration of a large number of alternative backbone structures. Results We derived a model to measure solvent accessibility with larger mutual information with residue types than previous models, optimized a set of rotamers which can approximate the sidechain atomic positions more accurately, and devised an empirical function to treat inter-atomic packing with parameters fitted to native structures and optimized in consistence with the rotamer set. Energy calculations have been accelerated by interpolation between pre-determined representative points in high-dimensional structural feature spaces. Sidechain repacking tests showed that ABACUS2 can accurately reproduce the conformation of native sidechains. In sequence design tests, the native residue type recovery rate reached 37.7%, exceeding the value of 32.7% for ABACUS1. Applying ABACUS2 to designed sequences on three native backbones produced proteins shown to be well-folded by experiments. Availability and implementation The ABACUS2 sequence design server can be visited at http://biocomp.ustc.edu.cn/servers/abacus-design.php. Supplementary information Supplementary data are available at Bioinformatics online.

A Load Sequence Design Method for Hydraulic Piston Pump Based on Time-Related Markov Matrix

2018 ◽  
Vol 67 (3) ◽  
pp. 1237-1248 ◽  
Author(s):  
Zhonghai Ma ◽  
Shaoping Wang ◽  
Chao Zhang ◽  
Mileta M. Tomovic ◽  
Tongyang Li
Keyword(s):  
Design Method ◽  
Piston Pump ◽  
Sequence Design ◽  
Hydraulic Piston Pump ◽  
Markov Matrix ◽  
Load Sequence

scholarly journals A Phase-Coded Sequence Design Method for Active Sonar

Sensors ◽  
2020 ◽  
Vol 20 (17) ◽  
pp. 4659
Author(s):  
Chengyu Guan ◽  
Zemin Zhou ◽  
Xinwu Zeng
Keyword(s):  
Matched Filter ◽  
Design Method ◽  
Design Methods ◽  
Time Lags ◽  
Specific Time ◽  
Sidelobe Level ◽  
Sequence Design ◽  
Active Sonar ◽  
Filter Performance ◽  
Periodic Autocorrelation

Phase-coded sequences are widely studied as the transmitted signals of active sonars. Recently, several design methods have been developed to generate phased-coded sequences satisfying specific aperiodic or periodic autocorrelation sidelobe level metrics. In this paper, based on the majorization–minimization strategy and the squared iterative acceleration scheme, we propose a method to generate sequences with the periodic weighted integrated sidelobe level metric. Numerical simulations illustrate that the proposed method can effectively suppress the periodic autocorrelation sidelobe levels in specific time lags. Compared with other sequence design methods satisfying the periodic weighted integrated sidelobe level metric, our method improves the computational efficiency significantly. In addition, the proposed sequence demonstrates better matched filter performance in specific range intervals compared with its counterpart. The results suggest that the method could be applied as a valid and real-time design method for transmitted signals of active sonars.

scholarly journals Passenger sequences can promote interlaced dimers in a common variant of the maltose-binding protein

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Afaque A. Momin ◽  
Umar F. Shahul Hameed ◽  
Stefan T. Arold
Keyword(s):  
Protein Tyrosine Kinase ◽  
Binding Protein ◽  
Protein Sequences ◽  
Maltose Binding Protein ◽  
Homologous Protein ◽  
Tyrosine Kinase 2 ◽  
Folding Dynamics ◽  
Protein Tags ◽  
Passenger Proteins

AbstractThe maltose-binding protein (MBP) is one of the most frequently used protein tags due to its capacity to stabilize, solubilize and even crystallize recombinant proteins that are fused to it. Given that MBP is thought to be a highly stable monomeric protein with known characteristics, fused passenger proteins are often studied without being cleaved from MBP. Here we report that a commonly used engineered MBP version (mutated to lower its surface entropy) can form interlaced dimers when fused to short protein sequences derived from the focal adhesion kinase (FAK) or the homologous protein tyrosine kinase 2 (PYK2). These MBP dimers still bind maltose and can interconvert with monomeric forms in vitro under standard conditions despite a contact surface of more than 11,000 Å2. We demonstrate that both the mutations in MBP and the fused protein sequences were required for dimer formation. The FAK and PYK2 sequences are less than 40% identical, monomeric, and did not show specific interactions with MBP, suggesting that a variety of sequences can promote this MBP dimerization. MBP dimerization was abrogated by reverting two of the eight mutations introduced in the engineered MBP. Our results provide an extreme example for induced reversible domain-swapping, with implications for protein folding dynamics. Our observations caution that passenger-promoted MBP dimerization might mislead experimental characterization of the fused protein sequences, but also suggest a simple mutation to stop this phenomenon.

Sign in / Sign up

Export Citation Format

Share Document