The structure of a protein is composed of a sequence of amino acid subunits that are joined together to form larger polypeptide chains. The amino acid side chains are the largest portion of the protein, while the hydrophilic R-groups are the smallest. The subunits are linked together by highly dynamic regions, which are associated with several important functional phenomena, such as allosteric regulation and enzyme catalysis.
Amino acid side chains
In addition to their polypeptide backbones, proteins also contain a number of side chains composed of various amino acids. The side chains vary in charge, shape, reactivity, and size, and can be nonpolar, hydrophobic, or polar. The various side chains are listed in Figure 3-3. The different side chains in proteins allow proteins to fold, function, and display various properties. This article will provide an overview of amino acids and their side chains.
In addition to side chains, proteins also have branched amino acids. Nonpolar amino acids are more preferred than longer, straight branched amino acids. Studies have shown that shorter, short branched hydrophobic amino acid chains are more conformationally flexible and stable in water. Therefore, proteins containing such amino acid side chains are more stable in both water and acids that are hydrophobic. This is important because long, straight branched hydrophobic amino acids will lead to protein fragmentation and breakage if they are exposed to extreme temperatures.
The amino acid side chains of proteins are non-polar or polar, depending on the type of alkyl groups they contain. A non-polar amino acid contains pure hydrocarbon alkyl groups. Examples of such amino acids are leucine and valine. While leucine is non-polar, alanine and valine contain aromatic rings. Aside from the non-polar side chains of amino acids, amino acid side chains have important effects on the biological process.
A number of recent studies have questioned the background pool of amino acids in nature. The chemoinformatics and structure-generation studies conducted by Meringer et al. (2013) suggest that a limited number of amino acids are naturally present in the a-carbon. Nevertheless, these results are not conclusive. They point to a need for a comprehensive analysis of amino acid side chains in proteins.
Hydrophilic R-groups
Water molecules have many functions in the body and many proteins contain both hydrophilic and hydrophobic R-groups. These groups interact positively with water molecules to stabilize a higher-order structure. The hydrophilic R-groups on a protein are buried deep within the folding macromolecule, while the hydrophobic groups are located far away from water molecules. They are responsible for maintaining the protein’s three-dimensional shape.
The nature of these R-groups can counteract the formation of hydrogen bonds within a protein. Those with like charges repel one another, while those with different charges attract. This is the process by which proteins form tertiary structures. These proteins have many R-groups that form complex three-dimensional structures. Hydrophilic R-groups are more abundant in the primary structure and the secondary structure.
The hydrophilic R-groups on proteins can also participate in the active site of an enzyme, or the portion of the enzyme that directly binds the substrate. Enzymes derived from proteins also contain catalytic groups that promote bond formation and degradation. Hydrophilic R-groups in proteins are typically not adjacent to each other in the primary or tertiary structure, but are neighboring in the polar-neutral moiety of the enzyme.
Standard amino acids are classified according to their polarity. Hydrophobic amino acids are blue, orange, and green, while hydrophilic amino acids are rose, yellow, and blue. Generally, hydrophobic amino acids are located in the center of the protein. Hydrophilic amino acids are found at the extremities of the protein, such as the cytoplasm. They are essential for the synthesis of proteins and other cellular structures.
Folding patterns
Proteins fold in a specific pattern based on the amino acid sequence in which each of the individual subunits is located. Folding occurs within milliseconds and is governed by the inter-amino acid interactions. Proteins have an astronomical number of configurations, with at least 10 to the power of 300 configurations possible. Scientists can only predict some of these folding patterns with certainty, unless they have the amino acid sequence of the protein.
Proteins are macromolecules and are formed from chains of amino acids joined by amide linkages. Folding patterns are determined by the amino acid sequence and the corresponding protein structure. A protein is likely surrounded by water and nonpolar hydrocarbon tails. Therefore, the asymmetric nature of protein structures limits their folding potential. The Ramachandran plot is one way of describing this restriction. Proteins can fold only in certain conditions if they can bend or rotate at a particular angle.
Another protein fold is known as a TIM barrel, which consists of eight a-helices alternating with eight b-strands. This structure is called after the enzyme triosephosphate isomerase. While TIM barrels are among the most commonly occurring protein folds, they have very little in common with each other in terms of sequence. Therefore, researchers are still trying to determine which structural motif best describes the function of a specific protein.
Scientists are trying to solve this challenge by developing better computational methods to predict how proteins fold. The AlphaFold program created by Google’s DeepMind is one example of an algorithm that can predict how proteins fold, and it has already defeated the world’s best Go, chess, and poker players. With its improved predictions, researchers can now use AlphaFold2 to design drugs for the first time and develop new biomaterials for human beings.
Folding patterns in intrinsically disordered proteins
The sequence of a protein reveals the degree of its intrinsic disorder. Many proteins have hydrophobic amino acid residues that drive their folding, but IDPs lack these, leaving them with a high proportion of polar amino acids. These proteins are characterized by the absence of a defined three-dimensional structure, but they display a rich variety of conformations that can serve a variety of functions.
The intrinsically disordered proteins, or IDPs, are incapable of folding into a stable structure, leading to their high degree of disorder and local mobility. Their high dynamic properties confer distinct functional advantages over proteins with a well-defined 3D structure. Molecular modeling and NMR studies have revealed the biological significance of these proteins, identifying their role in the pathophysiology of many diseases and healthy systems.
X-ray crystallography yields the majority of PDB structures, which often contain unresolved regions. This problem is compounded by the fact that most expression constructs remove the disordered regions so as to facilitate crystallization. Molecular dynamics simulations based on intrinsically disordered proteins will reveal the presence of regions that were previously neglected. The use of this technology will undoubtedly encourage more research on IDPs.
Because of the inherent low-free energy of binding, IDRs have a fine balance between the entropy cost of folding and the enthalpy gain of binding, and even small perturbations in entropy can cause IDRs to associate or dissociate from their interaction partners. In most cases, however, IDRs display weak but specific binding. In a few instances, the IDRs display tight binding. Furthermore, their association and dissociation rates vary considerably based on the mode of interaction.
Structure of a b sheet
A b-sheet of protein consists of two strands with hydrogen-bonding residues pointing in alternating directions. The linking loop between the two strands is almost always right-handed and b-sheets tend to exhibit an inherent twist. This structure is also associated with the b-hairpin motif, a simple structural motif that involves a loop containing glycine or proline, which is capable of assuming dihedral-angle conformations. It is commonly found in b-sheets and is the basic constituent of a TIM barrel.
The b-sheet forms when two or more polypeptide chain segments are lined up next to each other in a parallel arrangement. They are joined together by hydrogen bonds that form between amino and carbonyl groups. Moreover, the R groups extend above and below the plane of the b-sheet. Moreover, the strands are either parallel or antiparallel to one another. The N-termini of the peptide chain must match up in the same direction and the C-terminus must match up in opposite directions.
Molecular modeling has revealed that a b-sheet structure is the result of hydrogen bonding between amino acid residues. However, hydrogen bonding is difficult to obtain if the b-sheets are not in an optimal state. Hydrophobic interactions are needed to stabilize the b-sheet structure in water. Further, researchers have been studying related macrocyclic b-sheets that are capable of interacting with small proteins and retaining their structure.
The catalase crystal structure is a four-stranded antiparallel b-sheet with antiparallel hydrogen bonds. Its b-sheet structure is found in the PDB file 1GWE at 0.88 A resolution. In the edge-on view of the catalase crystal, the righthanded twist and pleat of the Cas protein are clearly visible. The amino acids with large ring structures are generally found in b pleated sheets, which allow ample space for side chains.
You may wonder: «Where are proteins made in a cell?». Here is some information about this process. Amino acids are the building blocks for protein production. Transfer RNA (tRNA) is a nucleic acid that binds to amino acids floating in the cell. A ribosome is responsible for attaching an amino acid to the tRNA. Next, the ribosome builds a polypeptide chain that will eventually be a large protein.
Ribosomes
In a cell, protein synthesis occurs within ribosomes. The ribosome is a complex cellular machine made of RNA molecules and proteins. These molecules are organized into two functional subunits, known as the large and small ribosomal subunits. These subunits work together to translate mRNA into proteins. They contain a similar shape but differ in size and structure.
The production of protein in a cell takes place in three stages: initiation, elongation, and termination. In each stage, amino acids are bonded to transfer RNA. Once the ribosome binds to an amino acid, it moves it along the mRNA, where it attaches to another amino acid. In time, the amino acid chain becomes a polypeptide, which will eventually form a larger protein.
In a cell, the ribosomes assemble polymeric protein molecules that are designed to perform a specific function. These molecules are essential for all living cells and their associated viruses. Ribosomes are located in the nucleolus of the cell. A cell’s nucleus contains information, while the cytoplasm provides construction materials for protein. Ribosomes are found in all organisms.
mRNA
The enzyme responsible for the synthesis of proteins is a ribosome, a small unit that locks on to the larger subunit. Unlike the larger subunit, which is a static unit, ribosomes can separate and break apart once the production of a protein is completed. They are also referred to as «mRNAs» and are composed of a mRNA and a protein.
The process of protein synthesis begins with the replication of DNA. DNA is the genetic instruction molecule, and mRNA is the strand that is copied into polypeptides. DNA and RNA are essential components of all cells, and the three types of RNA play critical roles in the pathway. The development of distinct functions for RNA is thought to be the molecular key to life. In the final section of this chapter, you will learn more about the biochemical events of protein synthesis.
The process of protein synthesis begins with the transcription of genes. RNA molecules are translated into amino acids by a specialized machine called ribosome. Afterwards, ribosomes take a set of amino acid sequences (known as codons). These amino acid sequences are then assembled into a protein, one amino acid at a time. This process continues until the ribosome encounters a «stop codon» — a sequence of three nucleotides with no amino acid.
peptidyl transferase
The mechanism of peptidyl transferase is not entirely clear. In principle, it requires two amino acids — an amine in the A site and an ester carbon in the P site — to link the tRNA. In addition to this, a water residue is present in the active site of peptidyl transferase. This water residue contains a reactive amino group (oxyanion). This group is negative because of an extra electron on oxygen. The hydrogen on water is partially positive and stabilizes the tetrahedral oxyanion intermediate.
The ribosome contains a peptidyl transferase enzyme in the large subunit of the ribosomal RNA. The P-site peptidyl transferase center catalyzes the formation of a covalent peptide bond between adjacent amino acids. It does this by using tRNAs. Both aminoacyl and peptidyl-tRNAs have different tRNAs, and the tRNAs are used during translation.
In a recent study, David et al. showed that protein synthesis takes place mainly in the nuclei. They used a novel method to determine the intracellular location of peptide synthesis. This method visualizes nascent polypeptides by labeling them with a puromycin tag. Puromycin tags remain on ribosomes, even in the presence of protein synthesis inhibitors. When protein synthesis inhibitors inhibit the production of mRNA, the ribosomes do not label peptidyl transferase. Therefore, they can be easily located by fluorescence microscopy using PMY-specific antibodies.
Transcription
The process of transcription involves copying DNA nucleotide sequences into RNA. RNA has a similar structure to DNA, but it only has one strand and uracil as its single base. This messenger RNA carries the message from DNA to the ribosomes. The message is then read by a carrier molecule called transfer RNA. The three letters of the message are then transcribed into the protein that the cell produces.
This process is the basis of gene expression. Transcription of proteins in cells allows genes to be expressed in the body. Proteins are made by interpreting the message contained in DNA. DNA is stored safely inside the nucleus of a cell, but messenger RNA is not. It is freely able to exit the nucleus and transports the message from the DNA template to the cytoplasm. DNA is an extremely stable molecule, while RNA is relatively unstable and prone to misreading.
A transcription factor helps the RNA polymerase bind to a promoter. Other transcription factors, known as activators, help the RNA polymerase bind to the promoter. The different types of proteins that control transcription are similar in their actions, but there are some important differences. A repressor protein prevents RNA polymerase from accessing DNA and is released when other molecules in the cell indicate gene expression. An activator protein, on the other hand, binds to signals before transcription begins.
Translation
The first step in protein synthesis is transcription, where genetic instructions from DNA are converted into a molecule called mRNA. The mRNA then carries instructions to a complex assembly of proteins known as ribosomes, located in the cell’s cytoplasm. Each tRNA molecule recognizes particular sets of three nucleotides in the mRNA, which are read from one end to the other. The ribosome then takes the amino acid sequence and assembles them into a protein chain. The translation of proteins takes place within the cell, and many proteins travel to the Golgiapparatus for further processing.
When the genetic code is translated, a group of three consecutive nucleotides called a codon is used as the basis of the protein. This sequence specifies which amino acid the protein will contain, and it also marks the beginning of the translation process. Once the chain of amino acids has been assembled, the other proteins in the cell join it to form a molecule called a polypeptide. After the polypeptide chain has been assembled, it folds into a three-dimensional structure and binds small molecules called cofactors.
The ribosome consists of two subunits, one called the small ribosomal unit and one called the large ribosomal subunit. The small ribosome is responsible for binding to the mRNA template, and the other, larger ribosomal subunit assembles with the small ribosomal unit. The ribosome steps along the mRNA, which is composed of two or three nucleotide «steps» in which the protein is translated. The final step in the translation process is the release factor, which binds the ribosomes and dissociates the ribosomes once translation is complete.
Molecular chaperones
Molecular chaperones are proteins that are produced in cells and play essential roles in various biological processes. These proteins are produced in cells to regulate the folding, transport, degradation, and signal transduction of proteins. The molecular chaperones are essential for proper functioning of cells and are found in all organisms. Hsps, which are also known as heat-shock proteins, are among the most important molecular chaperones.
While the Hsp70 and Hsp60 systems are the most studied chaperones, there are other types of chaperones, each with distinct cellular functions. Molecular chaperones modify polypeptide chains after they are formed. They alter the bonds between chains, as well as within and between them. Others may signal the cell’s protease system to break down damaged proteins. There is a growing body of research that links chaperone activity with neurodegenerative diseases.
Hsp70 belongs to the AAA+ family. It is a highly allosteric molecular machine that participates in cellular processes, including protein folding, refolding, and trafficking. The Hsp70 domain is enriched with hydrophobic and positively charged amino acids. The Hsp70 domain is known to control the ATPase cycle. BiP is a major folding factor in the ER, where it is essential for the secretion of proteins.
Structure of a multi-domain protein
The structure of multi-domain proteins in cells is often more complicated than the individual domains. The protein’s amino acid sequence can predict the structure. Mutations to the sequence alter the stability of a particular domain. When a single domain homologue is mutated, it undergoes non-polar to polar mutations to stabilize the fold. The mutations may also alter a sub-set of inter-domain interface residues.
To detect multi-domain protein structural analogues, a dedicated MPDB module is used. MPDB’s TM-align tool aligns individual domains onto protein models. This allows the analogue and native protein to be as close as possible. The Gscore measures structural similarity by comparing the model of an analogue to the protein in MPDB. The Gscore is a global score that evaluates the structural similarity between two protein structures.
A high-quality database of multi-domain proteins can make it easier to understand how they work. With this information, scientists can develop computational methods to model and predict multi-domain proteins in cell systems. Furthermore, a high-resolution multi-domain protein structure database will make investigations easier. It is also possible to use computational methods to model a single-domain protein in a cell. You can access this database by using AlphaFold2 or another similar program.
