scholarly journals Estimating the accuracy of the MARTINI model towards the investigation of Peripheral Protein-Membrane Interactions

2020 ◽  
Author(s):  
Sriraksha Srinivasan ◽  
Valeria Zoni ◽  
Stefano Vanni
Keyword(s):  
Membrane Proteins ◽  
Biological Processes ◽  
Cellular Membranes ◽  
Membrane Interactions ◽  
Peripheral Protein ◽  
Peripheral Membrane Proteins ◽  
Protein Membrane

Peripheral membrane proteins play a major role in numerous biological processes by transiently associating with cellular membranes, often with extreme membrane specificity. Because of the short-lived nature of these interactions,...

scholarly journals Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning

2021 ◽  
Author(s):  
Alexios Chatzigoulas ◽  
Zoe Cournia
Keyword(s):  
Machine Learning ◽  
Membrane Proteins ◽  
Ensemble Classifier ◽  
Binding Domains ◽  
Peripheral Membrane Proteins ◽  
Ensemble Machine Learning ◽  
Protein Interfaces ◽  
Protein Membrane ◽  
Membrane Interfaces ◽  
Membrane Attachment

Motivation: Abnormal protein-membrane attachment is involved in deregulated cellular pathways and in disease. Therefore, the possibility to modulate protein-membrane interactions represents a new promising therapeutic strategy for peripheral membrane proteins that have been considered so far undruggable. A major obstacle in this drug design strategy is that the membrane binding domains of peripheral membrane proteins are usually not known. The development of fast and efficient algorithms predicting the protein-membrane interface would shed light into the accessibility of membrane-protein interfaces by drug-like molecules. Results: Herein, we describe an ensemble machine learning methodology and algorithm for predicting membrane-penetrating residues. We utilize available experimental data in the literature for training 21 machine learning classifiers and a voting classifier. Evaluation of the ensemble classifier accuracy produced a macro-averaged F1 score = 0.92 and an MCC = 0.84 for predicting correctly membrane-penetrating residues on unknown proteins of an independent test set. Availability and implementation: The python code for predicting protein-membrane interfaces of peripheral membrane proteins is available at https://github.com/zoecournia/DREAMM.

scholarly journals Tug-of-war: molecular dynamometers against living cells for analyzing sub-piconewton interaction of specific protein with cell membrane

2021 ◽  
Author(s):  
Huipu Liu ◽  
Yunlong Chen ◽  
Jiawei Wang ◽  
Yuanjiao Yang ◽  
Huangxian Ju
Keyword(s):  
Membrane Proteins ◽  
Cell Membrane ◽  
Specific Protein ◽  
Living Cells ◽  
Membrane Interactions ◽  
Membrane Interaction ◽  
Protein Membrane ◽  
Functional Regulation ◽  
Signal Transductions

Protein-membrane interactions play important roles in signal transductions and functional regulation of membrane proteins. Here, we design a molecular dynamometer (MDM) for analyzing protein-membrane interaction on living cells. The MDM...

scholarly journals Computational identification of novel peripheral protein‐membrane interactions

2008 ◽  
Vol 22 (S1) ◽  
Author(s):  
Irina Kufareva ◽  
Felician Dancea ◽  
Mahadev Ravi Kiran ◽  
Zinaida Polonskaya ◽  
Michael Overduin ◽  
...  
Keyword(s):  
Membrane Interactions ◽  
Peripheral Protein ◽  
Protein Membrane ◽  
Computational Identification

scholarly journals Lipid Transporters Beam Signals from Cell Membranes

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 562
Author(s):  
Miliça Ristovski ◽  
Danny Farhat ◽  
Shelly Ellaine M. Bancud ◽  
Jyh-Yeuan Lee
Keyword(s):  
Membrane Proteins ◽  
Lipid Bilayers ◽  
Lipid Composition ◽  
Structural Integrity ◽  
Current Knowledge ◽  
Integral Membrane Proteins ◽  
Cellular Membranes ◽  
Cytoplasmic Proteins ◽  
Lipid Transporters

Lipid composition in cellular membranes plays an important role in maintaining the structural integrity of cells and in regulating cellular signaling that controls functions of both membrane-anchored and cytoplasmic proteins. ATP-dependent ABC and P4-ATPase lipid transporters, two integral membrane proteins, are known to contribute to lipid translocation across the lipid bilayers on the cellular membranes. In this review, we will highlight current knowledge about the role of cholesterol and phospholipids of cellular membranes in regulating cell signaling and how lipid transporters participate this process.

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