We are searching data for your request:
Upon completion, a link will appear to access the found materials.
Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y?
I guess A and B could be biomarkers of a certain disease, and in the pathological tissues their amount remains relatively unchanged but no longer interact, thus losing their functionality and causing the disease.
One possible condition would be that A and B don't interact directly but require a third protein C to act as the scaffold to form the complex A-C-B. So when C is expressed in tissue X but not in Y, we would observe this phenomenon.
Are there other mechanisms or examples?
Your example of an interaction mediated by a scaffold protein is certainly one way of controlling protein interactions. This doesn't just happen in different tissues either, it is also used to fine-control the interaction of certain proteins within one cell, the most notable example for this are the kinases in the MAP pathway (see for example this paper).
Another possibility I can see is that A and B can interact, but only if (at least) one of them is modified, e.g. by phosphorylation - so the actual interaction happens with A-p and B. In a case like this it's not unlikely that the protein that modifies A is only expressed (or active) in certain tissues, which then mean A(-p) and B can only interact in these tissues.
Deciphering cell–cell interactions and communication from gene expression
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein–protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand–receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell–cell interactions from transcriptomic data and review the methods and tools used in this context.
Protein interactomes across the tree of life
The following phylogenetic tree shows 1,539 bacteria, 111 archaea, and 190 eukarya. As ancestral species have gone extinct, older protein interactomes have been lost, and only interactomes of present-day species are available to us. For each species, we construct a separate PPI network, i.e., the protein interactome. An interactome captures all physical protein-protein interactions within one species, from direct biophysical protein-protein interactions to regulatory protein-DNA and metabolic interactions.
FOUNDATIONS FOR PROTEIN SYNTHETIC BIOLOGY
Synthetic Biology aims to prepare the ground for the routine engineering of complex biological systems ( 13, 15). The foundations for a protein synthetic biology are, in fact, more solid than for many other areas in this young field. A whole industry supports biochemists in the manipulation and production of recombinant proteins. Small-and large-scale initiatives provide atomic structures ( 16), electron microscopy ( 17) and other methods yield pictures of large assemblies and a wide range of biophysical methods are dedicated to the detailed study of protein function and dynamics. The experimental methods are complemented by a rich set of modeling tools. Quantum mechanic calculations describe fast reaction mechanisms at the subatomic level ( 18). Molecular mechanics strategies push the simulation of atomic dynamics into the microsecond time range ( 19). Higher order approximations ( 18) support rational design ( 20), virtual screening for binding partners ( 21) or the prediction of structures ( 22) and assembly geometries ( 23). Granted, none of this is easy. On the other hand, synthetic biologists have the luxury to cherry-pick well-characterized systems for which these methods actually work. A protein systems engineer can thus establish a near-complete chain of information from macroscopic quantities such as rate constants or stabilities down to subatomic detail. In contrast, most synthetic biology projects currently rely on the art of ‘black box engineering’ with only partial understanding of the systems they are dealing with. Synthetic gene networks, for example, depend on complex transcription and translation machineries and are subject to cell-state variation and other ‘side effects’. Protein-only circuits would be amenable to a more rational design approach—they could be optimized in vitro and be tested in solutions or extracts of increasing complexity before being employed to actual cells. RNA-based devices ( 24) or DNA computation systems ( 25) may offer similar levels of control and, like in natural cells, DNA, RNA and protein devices could in some future complement each other in synthetic systems ( 15).
The engineering of individual proteins has matured into a full-fledged scientific discipline with important applications. Traditionally, this field had been dominated by directed evolution methods which pan large pools of proteins with partly randomized sequence ( 26). More recently, computational protein design methods are becoming increasingly successful at the structure-based engineering of protein folds, interactions and activities ( 20). A combination of both approaches has recently culminated in the de-novo design of two enzymes ( 27, 28) with novel activities that are not found in nature. Increasingly though, protein engineers shift their attention from the manipulation of residues within individual globular proteins to the recombination and fusion of whole protein domains ( 29– 32).
Horizontal Cell Biology: Monitoring Global Changes of Protein Interaction States with the Proteome-Wide Cellular Thermal Shift Assay (CETSA)
The cellular thermal shift assay (CETSA) is a biophysical technique allowing direct studies of ligand binding to proteins in cells and tissues. The proteome-wide implementation of CETSA with mass spectrometry detection (MS-CETSA) has now been successfully applied to discover targets for orphan clinical drugs and hits from phenotypic screens, to identify off-targets, and to explain poly-pharmacology and drug toxicity. Highly sensitive multidimensional MS-CETSA implementations can now also access binding of physiological ligands to proteins, such as metabolites, nucleic acids, and other proteins. MS-CETSA can thereby provide comprehensive information on modulations of protein interaction states in cellular processes, including downstream effects of drugs and transitions between different physiological cell states. Such horizontal information on ligandmodulation in cells is largely orthogonal to vertical information on the levels of different proteins and therefore opens novel opportunities to understand operational aspects of cellular proteomes.
There are three functional categories of cell junction: adhering junctions, often called desmosomes tight, or occluding, junctions and gap, or permeable, junctions. Adhering junctions hold cells together mechanically and are associated with intracellular fibres of the cytoskeleton. Tight junctions also hold cells together, but they form a nearly leakproof intercellular seal by fusion of adjacent cell membranes. Both adhering junctions and tight junctions are present primarily in epithelial cells. Many cell types also possess gap junctions, which allow small molecules to pass from one cell to the next through a channel.
Diffusion can either be simple diffusion and be facilitated by another molecule
Simple diffusion is merely the movement of molecules along their concentration gradient without the direct involvement of any other molecules. It can involve either the spreading of a material through a medium or the transport of a particle across a membrane. All the examples given above were instances of simple diffusion.
The image is a simple representation of the diffusion of one particle in another medium.
Simple diffusion is relevant in chemical reactions, in many physical phenomena, and can even influence global weather patterns and geological events. In most biological systems, diffusion occurs across a semi-permeable membrane made of a lipid bilayer. The membrane has pores and openings to allow the passage of specific molecules.
On the other hand, facilitated diffusion, as the term indicates, requires the presence of another molecule (the facilitator) in order for diffusion to occur. Facilitated diffusion is necessary for the movement of large or polar molecules across the hydrophobic lipid bilayer. Facilitated diffusion is necessary for the biochemical processes of every cell since there is communication between various subcellular organelles. As an example, while gases and small molecules like methane or water can diffuse freely across a plasma membrane, larger charged molecules like carbohydrates or nucleic acids need the help of transmembrane proteins forming pores or channels.
The image shows the movement of an insoluble molecule from the extracellular space towards the cytoplasm.
Since they are relatively large openings in the plasma membrane, these integral membrane proteins also have high specificity. For instance, the channel protein that transports potassium ions has a much higher affinity for that ion than a very similar sodium ion, with nearly the same size and charge.
WHAT WILL WE LEARN?
Synthetic protein circuits will provide an acid test for systems biology methods and our understanding in general. A system that has been built from well-characterized parts according to human specifications leaves little excuse for failed predictions. In fact, we should be able to reconstitute synthetic protein circuits in vitro and study them with hardly any gaps in knowledge. Sequences and structures should be known, molecular dynamics can be simulated, rates and equilibrium constants can be measured and reactions can be modeled. Carefully controlled synthetic protein systems could therefore allow us to venture deep into the Terra incognita between structural and systems biology and study the interdependence of protein architecture, molecular dynamics and cellular signal processing.
Synthetic multicomponent protein systems may also become valuable research tools. A first generation of simple two-component protein interaction devices have found wide-spread use as sensors and controls throughout laboratories: yeast-two-hybrid ( 104) and related methods convert protein binding into gene expression and have revealed millions of physical interactions. Protein complementation devices ( 105– 107) provide alternative interaction readouts. The latest generation of drug- or even light-inducible interaction input devices ( 55, 57, 63) now allow researchers to intercept and manipulate cellular dynamics at high temporal and even spatial resolution. A few of these interaction input devices have already been combined with reusable output devices to give, for example, fine control over expression ( 57), proteolysis ( 127, 129) or intein splicing ( 113, 117). Examples are given in Tables 1 and 2.
The extracellular matrix
A substantial part of tissues is the space outside of the cells, called the extracellular space. This is filled with a composite material, known as the extracellular matrix, composed of a gel in which a number of fibrous proteins are suspended. The gel consists of large polysaccharide (complex sugar) molecules in a water solution of inorganic salts, nutrients, and waste products known as the interstitial fluid. The major types of protein in the matrix are structural proteins and adhesive proteins.
There are two general types of tissues distinct not only in their cellular organization but also in the composition of their extracellular matrix. The first type, mesenchymal tissue, is made up of clusters of cells grouped together but not closely adherent to one another. They synthesize a highly hydrated gel, rich in salts, fluid, and fibres, known as the interstitial matrix. Connective tissue is a mesenchyme that fastens together other more highly organized tissues. The solidity of various connective tissues varies according to the consistency of their extracellular matrix, which in turn depends on the water content of the gels, the amount and type of polysaccharides and structural proteins, and the presence of other salts. For example, bone is rich in calcium phosphate, giving that tissue its rigidity tendons are mostly fibrous structural proteins, yielding a ropelike consistency and joint spaces are filled with a lubricating fluid of mostly polysaccharide and interstitial fluid.
Epithelial tissues, the second type, are sheets of cells adhering at their side, or lateral, surfaces. They synthesize and deposit at their bottom, or basal, surfaces an organized complex of matrix materials known as the basal lamina or basement membrane. This thin layer serves as a boundary with connective tissue and as a substrate to which epithelial cells are attached.
New COVID-19 “Mexican Variant” Identified: Increasingly Spreading Across North America
It has recently become prominent in Mexico and, similarly to other variants, presents a mutation in the Spike protein of the coronavirus. The “Mexican variant” was identified by a research group of the University of Bologna.
A research group of the Department of Pharmacy and Biotechnology of the University of Bologna analyzed more than one million SARS-CoV-2 genome sequences. This analysis led to the identification of a new variant that, over the past weeks, has been spreading mostly in Mexico but has also been found in Europe. Their paper published in the Journal of Medical Virology presented the so-called “Mexican variant,” whose scientific name is T478K. Like other strains, this presents a mutation in the Spike protein, which allows coronaviruses to attach to and penetrate their targeted cells.
“This variant has been increasingly spreading among people in North America, particularly in Mexico. To date, this variant covers more than 50% of the existing viruses in this area. The rate and speed of the spread recall those of the ‘British variant,'” explains Federico Giorgi, who is the study coordinator and a professor at the Department of Pharmacy and Biotechnology of the University of Bologna. “The mutation of the Spike protein is structurally located in the region of interaction with human receptor ACE2. Coronaviruses attach to this receptor to infect cells, thus spreading the infection with more efficacy.”
The researchers started from the analysis of almost 1.2 million sequenced samples of the SARS-CoV-2 genome found in international databases until April 27, 2021. The new T478K variant was detected in 11435 samples. This is double the number of samples that presented the same variant just a month earlier. Such an increase since the beginning of 2021 alarmed the researchers.
The “Mexican variant” spreads evenly across males and females and age ranges. This variant represents 52.8% of all sequenced coronaviruses in Mexico, whereas in the United States it shows up only in 2.7% of the sequenced samples. As concerns Europe, the “Mexican variant” has spread feebly in Germany, Sweden, and Switzerland. In Italy it is virtually non-existent with only 4 reported cases.
The mutation characterizing this variant is located in a region of the Spike protein that is responsible for the interaction with the human receptor ACE2: this is the mechanism allowing coronaviruses to access the cells. Similar mutations are common to all variants that have been at the center of attention in the past months. Indeed, recent coronavirus variants stand out for their high infection rates, which made them pervasive in many areas of the world.
Researchers tested the action of T478K Spike protein with in silico simulations and found out that this mutated protein can alter the superficial electrostatic charge. Consequently, it can change not only the interaction with the ACE2 human protein but also with the antibodies of the immune system and thus hinder drug efficacy.
“Thanks to the great amount of data available in international databases, we can hold an almost real-time control over the situation by monitoring the spread of coronavirus variants across different geographical areas,” concludes Giorgi. “Keeping up this effort in the next months will be crucial to act promptly and with efficient means.”
“Preliminary report on SARS-CoV-2 Spike mutation T478K” is the title of the study published in the Journal of Medical Virology. The authors are Simone di Giacomo, Daniele Mercatelli, Amir Rakhimov, and Federico Giorgi, all from the Department of Pharmacy and Biotechnology of the University of Bologna.
Reference: “Preliminary report on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike mutation T478K” by Simone Di Giacomo, Daniele Mercatelli, Amir Rakhimov and Federico M. Giorgi, 5 May 2021, Journal of Medical Virology.