Cellular Signal Transduction

BCEM 547 Signal Transduction and Regulation of Metabolism

• Signal transduction is the biochemical processes by which cells respond to internal or external environmental cues.
• Key drug targets today include G-protein coupled receptors, protein kinases, proteases, and ion channels, which all play a role in signaling.
• To survive, cells communicate with neighbors, monitor conditions, and respond to stimuli impingement and intracellular changes and initiate appropriate responses.
• Cell signaling enables intercellular communication and organismal coherence.
• Cell signaling regulates cell expansion and division, which is critical for understanding malignant tumor development.

Cellular Crowding

• Cells communicate via extracellular messenger molecules.
• Endocrine system hormones circulate throughout the body to reach target cells.
• Intracellular signals respond to damage, initiating repair and coordinating cellular events.
• Cells monitor metabolites/nutrients for growth decisions which are linked to hormones such as insulin.
• Cells respond to extracellular messages via receptors that bind particular messenger molecules.

Messenger Molecule Binding and Signal Transmission

• Ligand binding to the extracellular surface relays a signal across receptor's cytoplasmic domain.
• If on the inner plasma membrane, the signal moves by 2 major routes, with 2 exceptions: Ligand-gated channels, Steroid hormone receptors.
• One receptor transmits signal from its cytoplasmic domain to a nearby enzyme which then generates a response.
• Second messengers are small substances that activate or inactivate specific proteins.
• Another receptor transforms its cytoplasmic domain into a cellular signaling response.
• Second messengers diffuse through the cytosol or embed in the membrane lipid bilayer depending on chemical structure.
• Outcome is similar whether the signal is through a second messenger or protein recruitment, activating a protein at the top of an intracellular signaling pathway.
• Each signaling pathway has a series of distinct operating proteins.
• Pathway proteins alter the conformation of subsequent proteins that either activate or inhibit the protein.
• Signals transmitted along such signaling pathways ultimately reach target proteins, altering gene expression, protein synthesis, metabolic activity, cytoskeleton reconfiguration, or cell motility.
• Finally, signaling must terminate for cells to respond to additional messages.

Proteoforms

• The term 'proteoform' designates the different molecular forms in which a single gene's protein product exists due to genetic variations, translation, proteolysis, RNA transcripts, unrecognized ORFs, and post-translational modifications.
• The functional translation of noncanonical human open reading frames expands the human proteome.
• Screening identifies micropeptides in the human genome.
• Protein translation that occurs outside of annotated open reading frames (ORFs) in messenger RNAs and within ORFs in long noncoding RNAs is pervasive.
• Micropeptides from short, upstream ORFs form protein complexes with canonical proteins encoded on the same messenger RNAs.
• 7264 noncanonical ORFs are identified in the human genome, ~3000 of these produce mini-proteins.

Post-Translational Modification of Proteins (PTMs)

• Covalent modifications of amino acid side-chains expand the functional and structural repertoire of proteins.
• PTMs create a limitless set of altered proteins.
• Reversible covalent modification mediates cellular response to changing conditions.
• Adding or removing a modification is fast and cheap, whereas making a protein is slower and more expensive.
• Proteins alter with methylation, acetylation, ubiquitylation/sumoylation of lysine residues, oxidation, or lipidation.
• Protein phosphorylation is the most common covalent modification.
• Ubiquitylation and acetylation ranked second and third.
• A polypeptide chain produces phospho-isoforms because it is phosphorylated at several sites, each with distinct activity.
• The same polypeptide chain is modified by different classes of PTMs which creates numerous variants.
• PTMs alter and control cell proteins.
• PTMs provide molecules for other proteins.

Reversible Protein Modification

• Covalent modifications serve as docking sites for domains in other proteins.
• Covalent modification relies on a sequence-specific context.
• The reversible modifications function as an element to send information.
• One enzyme "writes," another "erases," and another "reads" the message within a protein.

Protein Organization

• Proteins have modular construction from interaction, structural, and catalytic domains.
• Pathways that link receptors to targets involve protein-protein interactions.
• These interactions recruit signaling proteins to a subcellular location.
• A motif is a 3-10 residue sequence referred to as an SLIM.
• Protein-protein interaction domains are independently folding modules which can be expressed independently.
• N- and C-termini are usually spatially close, and the ligand-binding surface lies on the opposite face of the domain.
• This domain arrangement can insert into other proteins while projecting its ligand-binding site.

Interaction Domain Families

• Protein-protein interaction domains separate into sequence/ligand-binding related families.
• Src Homology 2 is P-tyrosine binding (SH2 and PTB). G-protein/GTP-binding is essential to cell surface receptors.
• Cytoplasmic proteins contain one or two SH2 domains to recognize motifs found on activated growth factor receptors.
• Surrounding amino acids are important.
• Initially, SH2 domains were identified as protein-tyrosine kinases parts in cancer-causing viruses.
• Interaction domains often mediate a type of molecular recognition.
• 120 SH2 domains.
• Phosphotyrosine-containing motifs are recognized by domains termed PTB (phosphotyrosine binding) domains, found on docking proteins such as IRS-1.
• P-serine/threonine binding includes 14-3-3, FHA, MH2 and BRCT, which recognize phosphoserine motifs, and mediate protein-serine/threonine kinase activities.
• Acetyl- and methyl-lysine binding involves acetylation or methylation of lysine residues creating binding sites for the proteins involved in chromatin remodeling.
• String domains/modules create new modular protein structures through organization. Different interaction domains are frequently founded within the same chain, and are able to create a multiple protein-protein, protein-phospholipid, p-carbo, and p-nucleic acid

Cell Receptors

• A large variety of molecules can function as extracellular carriers of information, including molecules like amino acids and amino acid derivatives, gases and steroids/eicosanoids.
• Extracellular signaling molecules recognize specific receptors on the surface of the responding cell.
• transmembrane α-helices can contain a family of receptors.
• They translate binding of signaling molecules into activation of GTP-binding proteins.
• Many receptors translate the presence of messenger molecules into changes inside the cell.
• RTKs activate receptor's protein-kinase activity in its cytoplasmic domain
• Protein kinases are active on autophosphorylating and create a docking platform.
• Some Ser/Thr receptor kinases exist, e.g., TGFẞ receptor.

G-Protein Coupled Receptors (GPCRs)

• GPCRs are so-named because they interact with G proteins and contain 7 transmembrane helices.
• Hundreds of different GPCRs have been identified in organisms and regulate extraordinary range of processes.
• They are the single largest protein encoded encoded by animal genomes, acting as a drug target of the pharmaceutical industry.
• Natural ligands that bind to GPCRs are diverse in hormones, chemoattractants, neurotransmitters, opium derivatives, odorants, tastants photons.

Intracellular Mechanisms of GPCRs

• When a receptor binds to a transmitter or hormone GPCR, it changes in it.
• A configuration passed across the membrane and causes a loops of receptor.
• The loops leads activate proteins to get a cytoplasmic surface to form a complex of G protein.
• The receptor interacts a shift confirm in cells a protein, where GTP makes then get active.
• A stage activate recptor number so signal amplificaiton by activating.
• After activate GPCR,it phosphyorlated after some ligand and sensitive to the GPCR phosphorylation
• A small of proteins called that bind to the protein and compete G protein-> and arrest the activation by protein.

Protein Kinases

• Kinases are produced to control phosphorylation that are are diffrent Strength of signal are determind so by subunit GTP.
• GTP after hydrolysized will go with subunit and trimeric and after complex it goes to resting state.
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Second Messengers

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Lipid-Derived Second Messengers

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Phospholipids

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Lipid Modification

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Protein Kinase

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G-Protein activation via phosphorylation

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Protein Kinases

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The Human kinome

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Global motif analysis

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GPCRs

• GPCR and its interactions with signal are to be understand for all processes
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Location Phosphoinositides

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PH domains in human proteins

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This covers the role of receptors in recognizing extracellular messages and initiating signal transduction. It also includes types of receptors, like ligand-gated channels and those activating enzymes. The different components and their functions in cell signaling are also covered.