PsePSSM-based Prediction for the Protein-ATP Binding Sites

2020 ◽  
Vol 15 ◽  
Author(s):  
Li Qian ◽  
Yu Jiang ◽  
Yan YuXuan ◽  
Chen Yuan ◽  
Tan SiQiao
Keyword(s):  
Feature Extraction ◽  
Fault Tolerance ◽  
Binding Sites ◽  
Binary Classification ◽  
Classification Problem ◽  
Position Specific Scoring Matrix ◽  
Atp Binding ◽  
Atp Binding Site ◽  
Promising Application ◽  
Scoring Matrix

Background: Predicting the protein-ATP binding sites is a highly unbalanced binary classification problem, and higher precision prediction through the machine learning methods is of great significance to the researches on proteins’ functions and the design of drugs. Objective: Most existing researches typically select 17aa as the length of window by experience, and extract features by the Position-specific Scoring Matrix (PSSM), and then construct models predicting with SVC. However, the independent prediction values obtained in these researches are either over-high(ACC) or lower(MCC), and there is therefore larger improving room in the prediction precision. Methods: This paper utilizes the mutual information, I, to define the window length of 15aa, and the Pseudo Position Specific Scoring Matrix (PsePSSM), which is more fault-tolerance, to extract the features, and then trains multiple 1:1 SVC classifiers to model, and finally performs the simple votings. Results: The prediction results over two protein-ATP binding site datasets, the ATP168 and the ATP227, are totally superior to the independent prediction results obtained in the Reference Feature Extraction Approach. And in our approach, the MCC values are respectively improved, from the range of 0.3110 ~ 0.5360 and the range of 0.3060 ~ 0.553, to 0.7512 and 0.7106. Conclusion: Further, we explain why the PsePSSM approach is more fault-tolerance. This approach has a promising application prospect in the feature-extraction of protein sequences.

scholarly journals A Variable Domain near the ATP-Binding Site in Drosophila Muscle Myosin Is Part of the Communication Pathway between the Nucleotide and Actin-binding Sites

2007 ◽  
Vol 368 (4) ◽  
pp. 1051-1066 ◽  
Author(s):  
Becky M. Miller ◽  
Marieke J. Bloemink ◽  
Miklós Nyitrai ◽  
Sanford I. Bernstein ◽  
Michael A. Geeves
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Variable Domain ◽  
Actin Binding ◽  
Atp Binding ◽  
Atp Binding Site ◽  
Communication Pathway ◽  
Muscle Myosin

PSSM-Suc: Accurately predicting succinylation using position specific scoring matrix into bigram for feature extraction

2017 ◽  
Vol 425 ◽  
pp. 97-102 ◽  
Author(s):  
Abdollah Dehzangi ◽  
Yosvany López ◽  
Sunil Pranit Lal ◽  
Ghazaleh Taherzadeh ◽  
Jacob Michaelson ◽  
...  
Keyword(s):  
Feature Extraction ◽  
Position Specific Scoring Matrix ◽  
Scoring Matrix

Protein Structural Class Prediction viak-Separated Bigrams Using Position Specific Scoring Matrix

2014 ◽  
Vol 18 (4) ◽  
pp. 474-479 ◽  
Author(s):  
Harsh Saini ◽  
◽  
Gaurav Raicar ◽  
Alok Sharma ◽  
Sunil Lal ◽  
...  
Keyword(s):  
Amino Acids ◽  
Feature Extraction ◽  
Tertiary Structure ◽  
Position Specific Scoring Matrix ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Protein Functions ◽  
Scoring Matrix ◽  
Feature Extraction Technique

Protein structural class prediction (SCP) is as important task in identifying protein tertiary structure and protein functions. In this study, we propose a feature extraction technique to predict secondary structures. The technique utilizes bigram (of adjacent andk-separated amino acids) information derived from Position Specific Scoring Matrix (PSSM). The technique has shown promising results when evaluated on benchmarked Ding and Dubchak dataset.

Fluorometric study on conformational changes in the catalytic cycle of sarcoplasmic reticulum Ca2+-ATPase

1995 ◽  
Vol 15 (5) ◽  
pp. 317-326 ◽  
Author(s):  
Tohru Kanazawa ◽  
Hiroshi Suzuki ◽  
Takashi Daiho ◽  
Kazuo Yamasaki
Keyword(s):  
Sarcoplasmic Reticulum ◽  
Binding Site ◽  
Conformational Changes ◽  
Binding Sites ◽  
Transmembrane Domain ◽  
Tryptophan Fluorescence ◽  
Cytoplasmic Domain ◽  
Catalytic Cycle ◽  
Atp Binding ◽  
Atp Binding Site

Changes in the fluoresence of N-acetyl-N′-(5-sulfo-1-naphthyl)ethylenediamine (EDANS), being attached to Cys-674 of sarcoplasmic reticulum Ca2+-ATPase without affecting the catalytic activity, as well as changes in the intrinsic tryptophan fluorescence were followed throughout the catalytic cycle by the steady-state measurements and the stopped-flow spectrofluorometry. EDANS-fluorescence changes reflect conformational changes near the ATP binding site in the cytoplasmic domain, while tryptophan-fluorescence changes most probably reflect conformational changes in or near the transmembrane domain in which the Ca2+ binding sites are located. Formation of the phosphoenzyme intermediates (EP) was also followed by the continuous flow-rapid quenching method. The kinetic analysis of EDANS-fluorescence changes and EP formation revealed that, when ATP is added to the calcium-activated enzyme, conformational changes in the ATP binding site occur in three successive reaction steps; conformational change in the calcium enzyme substrate complex, formation of ADP-sensitive EP, and transition of ADP-sensitive EP to ADP-insensitive EP. In contrast, the ATP-induced tryptophan-fluorescence changes occur only in the latter two steps. Thus, we conclude that conformational changes in the ATP binding site in the cytoplasmic domain are transmitted to the Ca2+-binding sites in the transmembrane domain in these latter two steps.

scholarly journals Adenosine nucleotide binding sites on Complex V from diverse organisms

2021 ◽  
Author(s):  
Abhinav Parashar ◽  
Kelath Murali Manoj
Keyword(s):  
Binding Sites ◽  
In Silico ◽  
Nucleotide Binding ◽  
Atp Binding ◽  
Atp Binding Site ◽  
In Silico Docking ◽  
Epsilon Subunit ◽  
Nucleotide Binding Sites ◽  
Alpha Beta ◽  
Adenosine Nucleotide

Using in silico docking approaches, we scan the various subunits of Complex V (FoF1ATPase) for putative adenosine nucleotide binding sites. We find that multiple generic ADP/ATP binding sites are present on the alpha-beta binding sites and a conserved ATP binding site is present on the epsilon subunit. These findings support the murburn model of Complex V.

scholarly journals ATP-binding sites in brain p97/VCP (valosin-containing protein), a multifunctional AAA ATPase

2003 ◽  
Vol 374 (2) ◽  
pp. 473-480 ◽  
Author(s):  
Ran ZALK ◽  
Varda SHOSHAN-BARMATZ
Keyword(s):  
Conformational Changes ◽  
Binding Sites ◽  
Covalent Binding ◽  
Protein A ◽  
Atp Binding ◽  
Amino Acid Sequencing ◽  
Protein Determination ◽  
Atp Binding Site ◽  
Aaa Atpase ◽  
Nucleotide Specificity

VCP (valosin-containing protein) or p97 is a member of the AAA family (ATPases associated with a variety of cellular activities family), a diverse group of proteins sharing a key conserved AAA module containing duplicate putative ATP-binding sites. Although the functions of the AAA family are related to their putative ATP-binding sites, the binding of ATP to these sites has not yet been demonstrated. In the present study, the ATP-binding site(s) of brain VCP was characterized using the photoreactive ATP analogue, BzATP [3′-O-(4-benzoylbenzoyl)ATP]. Photo-activation of Bz-[α-32P]ATP resulted in its covalent binding to a 97-kDa purified soluble or membrane-associated protein, identified by amino acid sequencing as VCP. Bz-[α-32P]ATP covalently bound to the purified homo-hexameric VCP with an apparent high affinity (74–111 nM). A molar stoichiometry of 2.23±0.14 BzATP bound per homo-hexameric VCP (n=6) was determined using different methods for analysis of radiolabelling and protein determination. Nucleotides inhibited the binding of Bz-[α-32P]ATP to VCP with the following efficiency: BzATP>ATP>ADP≫adenosine 5′-[β,γ-imido]triphosphate≥adenosine 5′-[β,γ-methylene]triphosphate, whereas AMP, GTP and CTP were ineffective. VCP was observed to possess very low ATPase activity, with nucleotide specificity similar to that for BzATP binding. Conformational changes induced by an alternating site mechanism for ATP binding are suggested as a molecular mechanism for coupling ATP binding to the diverse activities of the AAA family.

Comparative Studies on the ATP-Binding Sites in Ca2+-ATPase and (Na+ + K+)-ATPase by the Use of ATP-Analogues

1982 ◽  
Vol 37 (7-8) ◽  
pp. 692-705 ◽  
Keyword(s):  
Atpase Activity ◽  
Binding Sites ◽  
Sulfhydryl Groups ◽  
Atp Binding ◽  
Stable Form ◽  
Atp Binding Site ◽  
Atp Analogues ◽  
Transport Atpases ◽  
High Concentrations ◽  
Hydrolysis Of

Abstract The effects of ATP-analogues on Ca2+-ATPase and (Na+ + K+)-ATPase have been studied. The participation of sulfhydryl groups in the recognition of ATP by both transport ATPases is indicat ed by the fact, that the disulfide of thioinosine triphosphate inactivates both enzymes. The reactivity of rapidly and slowly reacting sulfhydryl groups in the ATP binding sites of both enzymes is altered by the presence of transport substrates. At least in (Na+ + K+)-ATPase Na+ and Mg2+ appear to alter the structure of the ATP binding site, which conclusion is fortified by the fact, that the photoinactivation of the enzyme by 3′-O-[3-(2-nitro-4-azidophenyl)-propionyl]-ATP need Mg2+. Chromium(III)ATP, a MgATP analogue, inactivated both transport ATPases by the formation of a stable chromo-phosphointermediate. In the case of Ca2+-ATPase this was concomited by the occlusion of Ca2+ in a stable form. No occlusion of Na+ was observable so far in the (Na++ K+)-ATPase. Contrary to the expectation of the Albers-Post-scheme the hydrolysis of the phosphointermediate formed from chromium(III)ATP was protected by K+, but activated by high concentrations of Na+. Consequently, despite of the inhibition of (Na+ + K+)-ATPase activity chromium(III)-ATP supported the Na+ - Na+ -exchange reaction in everted red bood cells.

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