Classification of DNA Minor and Major Grooves Binding Proteins According to the NLSs by Data Analysis Methods

Abstract

High-mobility group proteins are a superfamily of DNA-binding proteins that bind to the DNA minor groove and bend it, whereas most of the transcription factors such as centromere protein B (CENP-B), octamer (Oct)-1, growth factor independence 1 (Gfi-1), and WRKY bind to the major groove of DNA. Classification of proteins using their DNA-binding features is the aim of this study. Nuclear localization signals play more important roles in entering DNA-binding proteins to nucleus and doing their functions; therefore, they have been considered as a feature which is important for DNA-binding manner in proteins. Nuclear localization signals (NLSs) were predicted by two prediction web servers, and then, their sequence ordered features were extracted by Chou's pseudo amino acid composition (PseAAC) and ProtParam. Multilayer perceptron was used as an artificial neural network for analyzing the features by calculating the correlation coefficient and 30-fold cross-validation. Another used data-analyzing program was principal component analysis of the Minitab software. By calculating the eigenvalues and considering five principal components, the sequence length of NLSs was known as the best feature for classifying DNA-binding proteins. Minimum mean squared error (MSE) (0.1098) and the highest R (2) (0.963) mean that there is a significant difference between the NLS length of the DNA major groove and minor groove binder proteins. Results showed that it is possible to classify DNA major groove and minor groove binder proteins by their NLS sequences as a feature.

Retention of nucleic acids in ion‐pair reversed‐phase high‐performance liquid chromatography depends not only on base composition but also on base sequence

“…How do these proteins bind to dsDNA? The key points are the major grooves and minor grooves in dsDNA (see DNA structure in https://en.wikipedia.org/wiki/DNA), induced by the contortion of base‐stacking and sugar‐phosphate skeleton, which lead to an exposure of functional groups and provide the structure basis for the protein‐DNA interaction . Besides proteins, small molecules (drugs) can also interact with DNA through major and minor grooves , some of which are used in the treatment of cancer.…”

TMPyP binding evokes a complex, tunable nanomechanical response in DNA

“…DNA nanomechanics are influenced by DNA-binding molecules that interact with DNA in a variety of ways (9-13). Certain proteins and small molecules bind to the major or minor grooves of dsDNA, thereby altering its structure (14) and stability (10,(15)(16)(17)(18)(19)(20). Others may display electrostatic or allosteric interactions with DNA, but neither of them results in the disrupting of genome continuity (10).…”

High Mobility Group Proteins in Sepsis

“…HMGs are the most abundant nuclear proteins except histones, and are widely expressed in tissues and organs ( 8 ). HMGs can bind distorted DNA uniquely and play a key role in transcription, recombination and DNA repair ( 9 ). HMGs are implicated in the pathogenesis of multiple diseases, including traumatic shock, infection, cancer, diabetes and autoimmune diseases ( 10 – 12 ).…”