Disease Prediction and Drug Development
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam in Introduction to Computational Health Informatics, 2019
Proteins in the final form have a 3-D folding pattern that can be altered dynamically due to the presence of another protein or another small biomolecule that binds to a receptor on the surface of the protein. This protein–protein interaction or protein interaction with other molecules alters the original functionality of a protein. There are many types of receptors on the surface of a protein. Some receptors bind to specific classes of proteins, while others may be generic. Antigens bind to these receptors to change the behavior of the proteins. In response to the docking of the external biomolecule, a protein 1) may change 3D-configuration that alters its functionality; 2) split in two parts changing the functionality and 3) change the reaction-rate.
Signal transduction and exercise
Adam P. Sharples, James P. Morton, Henning Wackerhage in Molecular Exercise Physiology, 2022
The above mechanisms are linked such that several of the individual mechanisms contribute to each step of signal transduction. For example, protein-protein interaction is necessary for one protein to bind and modify the next. The change in protein shape due to modification may then expose a localisation signal that causes the protein to translocate. In some cases, posttranslational modification causes translocation to the nucleus and affects gene transcription. In the case of ubiquitination, modification causes translocation to the proteasome where the protein is degraded, and this terminates the signalling event. For the sake of clarity, we will discuss the transduction processes individually in more detail below with specific examples of molecular regulation in exercising skeletal muscle.
An Analysis of Protein Interaction and Its Methods, Metabolite Pathway and Drug Discovery
Ayodeji Olalekan Salau, Shruti Jain, Meenakshi Sood in Computational Intelligence and Data Sciences, 2022
According to the environment of a broad area of protein, various efficient methods are to be improved to predict protein interactions. Some of the new ethics belong to the existing methods with developed techniques. It helps to know how to use the interpreted methods in experimental processes for the protein interaction prediction [85]. Figure 13.9 shows the encoded genetic method for cross-linking studies of ncAAs for protein interaction with ribosomal interpretation of live cells. It contains the suppressor tRNA with orthogonal AARS charges of ncAAs, that delivers to the ribosome, which incorporates to a responsible in-frame amber codon with nascent protein. In this way cross-linking ncAA characterize the protein features. Protein interaction helps to identify the mechanism of infection, drug development and the solution to the infection with treatment [86]. In protein–protein interaction relates to target regions and it helps to identify the functions and drug design of the proteins [87]. The SIM tool is used to find the site of the protein interaction with the unbounded protein structures [88]. By using interacting and non-interacting pairs of proteins, structural features are classified into binding or unbinding behaviour of proteins [89].
Gankyrin: a novel promising therapeutic target for hepatocellular carcinoma
Published in Artificial Cells, Nanomedicine, and Biotechnology, 2018
Parvin Zamani, Maryam Matbou Riahi, Amir Abbas Momtazi-Borojeni, Khadijeh Jamialahmadi
Protein–protein interactions have a fundamental role in the regulation of biological systems. Therefore, disrupting the interaction between two proteins has a vital importance in the development of disease states. The discovery and development of small-molecule drugs that can directly disrupt protein–protein interactions has been developed over the last decade. Generally, these small molecules can disrupt the interaction between two protein partners with direct binding to interface of one protein partner to pockets site on the surface of another protein partner through an allosteric mechanism, or binding to a catalytic site. Therefore, the main function of these small molecule inhibitors is that mimicking frame essential structure in the globular protein in the protein–protein complex interactions [111].
Targeting thermoTRP ion channels: in silico preclinical approaches and opportunities
Published in Expert Opinion on Therapeutic Targets, 2020
Gregorio Fernández-Ballester, Asia Fernández-Carvajal, Antonio Ferrer-Montiel
Protein–protein interactions are at the core of normal and pathogenic cell biology and physiology. Abnormal protein–protein interactions drive signaling changes that are behind several pathologies [55]. Despite limitations for the use of peptides as drugs targeting thermoTRP channels, there is a long list of peptides currently available or waiting for clinical approval, that are mainly derived from natural sequences. This proves that peptides are versatile molecules used for the treatment of pathologies such as allergy, inflammation, arthritis, immune and cardiovascular diseases, osteoporosis, and pain. Targeting protein–protein interactions in thermoTRP channels may be convenient since peptide-based drugs tend to increase drug selectivity, thus reducing the adverse effects of low pharmacological specificity [107]. However, these peptides normally display lower bioavailability, particularly oral.
Proteomic studies of common chronic pain conditions - a systematic review and associated network analyses
Published in Expert Review of Proteomics, 2020
The proteomic approach provides enormous amounts of raw data that can be handled with the help of bioinformatic tools such as STRING (Search Tool for Retrieval of Interacting Genes/Proteins), which is available on the World Wide Web [67]. The output of proteomic studies is often a panel of multiple proteins instead of single proteins. The majority of the identified proteins do not function independently, because they regulate activity and induce/reduce expression levels of other proteins, it is reasonable to study protein-protein interactions to better understand the physiology and the biological processes proteins affect. Gomez-Varela et al. suggest using the term protein disease signatures (PDS) rather than biomarkers – PDS is loosely defined as proteins that differ between disease conditions and controls [68]. A network construction is needed that can organize the large amount of proteomics data, a prerequisite for the identification of the underlying mechanisms of chronic pain conditions [69,70]. Once the interesting pathways and functions are identified, a hypothesis can be created that considers the specific proteins involved in chronic pain.
Related Knowledge Centers
- Protein
- Molecular Machine
- Interactome
- Creutzfeldt–Jakob Disease
- Alzheimer's Disease
- Methods to Investigate Protein–Protein Interactions
- Biochemistry
- Molecular Dynamics
- Signal Transduction
- Metabolic Network