Protein: Structure and Function

Protein: Structure and Function

Abstract

Proteins are amino acids covalently connected by peptides to form a sequence.  In cells, proteins play an important role such as transporting ions and molecules within the membrane, catalysts or enzymes, and structural functions among others. There are about twenty amino acids that constitute essential proteins. Of these amino acids, each one has an elemental structure that consists of central carbon known as alpha carbon, which is bonded to hydrocarbon, amino group, carboxyl and a distinct side sequence or the R-group. The main feature that distinguishes a given amino acid from others is the individual side series or R-group, an aspect that characterizes its chemical elements.  The distinct side series or R-group presents unique chemical features of amino acids while dictating how they bond with each other in proteins. Therefore, amino acid can be categorized as hydrophobic opposed to hydrophilic, and uncharged vs. positive vs. negative charge. The 3D conformation of protein action is determined based on the compound binding with side chains. Particular characteristics can be construed by assessing the elements of amino acid clusters. This review sets out to highlight protein structures and functions.

Introduction

Even though proteins are distinct, they have standard features (Figure 1). The primary fabric of every protein is assessed by categorization of amino acids, encrypted by mRNA in charge of directing correct folding of polypeptide sequence to form secondary structure. [2] One of the types of protein structure is an alpha helix, a section of a polypeptide that primarily folds into the corkscrew structure. Beta strands are linear in the shape of polypeptides, which bond into a flat beta sheet. Also, other sections of the secondary structure can encompass turns as well as random strands. Such strands, helices, coils and turns chemically bond into unique 3D structure of proteins, known as a tertiary structure. [3] For individual proteins, a single polypeptide structure, folds to form 3D shape creating a final protein. A variety of proteins, nevertheless, have some polypeptide subunits that activate the final protein. For such proteins, the bonding among various subunits folds into quaternary shape.
Detached percentages of proteins have the ability to crinkle individually from other proteins, and they have their roles. These are usually known as domains and act as part of foundations of that protein. Domains are not only evolutionarily but also movable, and can reorganize as novel proteins develop. There are countless structural domains, and several of them have been preserved extensively across protein. New proteins seem having risen over evolutionary time through the integration of different areas in a procedure called domain shuffling. In most cases, the domain has small designs, which involve preserved amino acids or arrangements of structural components created through folding of close by amino acid chains. [4] For example, the helix-loop-helix that binds with DNA.  Similar patterns are present in various proteins, which are not linked. Experts have categorized domain and patterns in different databases demonstrating that protein can easily be evaluated to determine the presence of such compounds. [15]

Figure 1. Protein structure. Primary structure; particular chain of amino acids in a protein sequence. Secondary structure: polypeptide sequence folds to form distinct patterns like alpha helix and beta pleated sheet. Some sections of secondary structure can comprise of random coils and turns. Tertiary composition: The distinctive 3D shape that results from the chemical reaction with amino acids to form folds in secondary design. Quaternary Structure:  the particular reaction between or two or many polypeptide subunits.
Moreover, a collection of protein in the cell helps in determining its functions and health. Proteins are in charge of almost each task in cells including structure of the cell, internal organization, cleanup of waste, regular maintenance, and product manufacturing. [1, 4] Proteins receive external signals while mobilizing intracellular reactions. In short, proteins are workhorse macromolecules of cells, and also different from the roles they play as shown in Figure 2.

Figure 2:  Protein phosphorylation can make them either active (orange) or inactive (green). The enzyme responsible for causing phosphorylation is Kinase while Phosphatase dephosphorylates. In other words, Phosphatase effectively undoes the activity of the kinase.
Proteins can either be large or minute, nearly hydrophobic or hydrophilic, existing solely or as elements of multi-unit pattern and change design often or virtually stationary. [5, 6] These differences come about, as a result, distinct amino acids chains that form proteins. Additionally, totally folded proteins have unique surface features that are important in determining molecules with which to bond. [13] During bonding, protein conformation may modify in subtle or remarkable manners.
Needless to say, protein functions and structure are different. For instance, protein structure plays an essential role in maintaining the shape of cells and comprise structural components within connective tissues such as cartilage. Another category of protein is enzymes, which catalyze biochemical reactions occurring within cells. Whereas other proteins function as monitors, they can modify their structures and activities based on metabolic response or notifications from external cells. [7] On the other hand, cells secrete different proteins that form an extracellular matrix or in charge of intracellular communication.
Proteins modification takes the completion of translation and folding.

In this case, the transferase enzymes add modifiers like carboxyl or phosphates to proteins. [8] Such changes can shift protein conformation and serve as molecular buttons that help in turning on or off protein activities. Some post-translation changes are reversible though diverse enzymes can catalyze reverse activities. For instance, kinases add phosphate to proteins while phosphatases play the role of eliminating phosphates groups Figure 3.

Figure 3: proteins role in providing structural support in cells. Actin and microtubule are two proteins in change of providing structural support in cells

Peptides and Proteins

While amino acids are serial covalent bonds of peptides, the sequence is usually 30 amino acids less, making the bond shorter in dimension. As such, it is referred to as the peptide. However, longer amino acids are known as polypeptides. [14] Furthermore, peptide bonds are created between carboxyl of a given amino acid and the amino group of the subsequently amino acid. On the other hand, the formation of peptide bond takes place in condensation effect involving the loss of water.

The head-tail pattern of amino acid in protein implies that there is an amino cluster on one end known as amino terminus and carboxyl on the other end or carboxyl terminus.

Levels of Protein Structure

Structural characteristics of proteins come in various complex levels.
•    Primary structure: this is a linear pattern of amino acids in protein as well as the position of covalent connections including disulfide interactions among amino acids.
•    Secondary structures: this is the folding sections within proteins such as pleated sheets that are stabilized through carbon binding.
•    Tertiary structure: this is the ultimate 3D shape of proteins that develop from a vast number of non-covalent bonding among amino acids.
•    Quaternary arrangement: this is the non-covalent binding in charge of connecting various proteins to form a single and large protein such as Hemoglobin. [13] This is because it has the interactions of two alpha globin as well as beta globin polyproteins.
By and large, the primary arrangement of protein can be construed from nucleotide chain of corresponding messenger RNA. [12] According to the primary pattern, several characteristics of secondary structure may be forecasted using computer applications. Nevertheless, forecasting protein tertiary structure continues to be challenging, though some advancement have been initiated in this area.
Protein function in biochemical reactions
Cells depend on various enzymes to catalyze metabolic activities. Since enzymes are proteins, they facilitate biochemical reactions by reducing activation energy, thus making cell process faster compared to no catalysts. In essence, enzymes are significantly particular to their deposit. They interact with these deposits at complementary regions on surfaces, acting as a basis for presenting a fitting similar to locks and keys. For that reason, they function by interacting with more deposits, merge them to ensure that reactions occur and release them upon completion of the reaction. When deposit interactions take place, enzymes go through a conformational change that adjust or strain them to make more reactive (Figure 4).

Figure 4:  Catalytic and activation energy
Enzymes reduce activation energy essential in changing reactant to form a product.  The figure (red) on the left demonstrates unanalyzed reaction. [10] In an enzyme-catalyzed activity, enzymes interact with reactant while facilitating its modification to form a product. Subsequently, the enzyme binds to the reactant and facilitates its transformation into a product. Consequently, the enzyme-catalyzed activity pathway has less activation energy to rise above prior to the progression of the reaction. [14] Furthermore, in the plasma membrane, protein plays the role of interacting with cells. [8,9] For instance, plasma membrane protein performs various tasks as transporting nutrients, receive chemical communication, convert chemical signals to form intracellular activity and under certain conditions anchor cells in a particular position. [4.5]

Proteins and Proteomics.

The 3-D arrangement of a protein illustrates not only its size and form but its task as well.  One attribute that influences activity is the hydrophobicity of protein defined by the primary and secondary arrangement. For instance, a close review of the membrane protein shows that these membranes comprise large amounts of lipids that are extremely hydrophobic amino acids. [9, 13] These water repellant areas interconnect constructively with hydrophobic lipids in the tissue to form stable tissues structures.
Hemoglobin, which is a solvable protein inhibits the cytoplasm of red blood cells as solitary molecules that fuse with oxygen transporting it to the membranes. [3, 7] In sickle cell anemia, for instance, alterations in the beta-globin of the red blood cells escalate its hydrophobicity causing the transmuted protein molecules cling to each other, circumventing the aqueous solution. [15] Hemoglobin restraints change the form of the red blood cell from round to a sickle shape, causing the cells to gather in constricted blood veins.
The wrinkling of a protein necessitates for the binding of amino acids detached from each other in the core arrangement of the protein. These amino acids create a mechanism that aggravates the catalytic reaction. [1] This region, known as the active area of the enzyme, has amino acids that interact explicitly to the substrate molecule known as a ligand (Figure. 5). In the same breadth, particular areas in cell receptor proteins interlink with individual ligand elements that receptor identifies. [4, 6] Variations in amino acids that are far apart in the primary arrangement can cause mutations in folding. It might also alter amino acids chemical binding especially at an active region, which may affect the catalyst processes or interaction of the ligands to receptor proteins. [8, 10]

Figure 5: Active Area
Figure 5: The dynamic area of the penicillin-binding protein. The grim-like arrangement embodies the secondary as well as tertiary configuration of the penicillin-interaction protein. [2, 4] The interaction of the antibiotic, the residue, to the vibrant region units prevent the standard action of the protein in the microbe cell, leading to the death of the cell.

Discussion.

Genes encrypt proteins by presenting an arrangement of nucleotides decoded into a structure of amino acids. [1] The amino acid arrangement is referred to as the primary configuration of the protein. Nonetheless, to work effectively, this amino acid network should crinkle into a composite 3D form. Protein crinkling entails the development of local physical designs like helices and 9panes (secondary arrangements) and the union of these distinct configurations into a collective 3-D arrangement known as the tertiary. [7, 12] The utmost accomplishment of the human gene stems from its capacity to encrypt the precise 3-D shapes of innumerable proteins by way of linear classifications. Protein configuration is fundamental for accurate function because it permits molecular identification.
For instance, enzymes are proteins that accelerate chemical processes. The purpose of an enzyme depends on the arrangement of its dynamic area, a fissure in the protein with a form and dimension that allows it to fit the expected substrate very tightly. [1, 14]
The operations of an enzyme depend on the structure of its dynamic region, a fissure in the protein with form and dimension that allows it to fit the projected substrate very cozily. [2] With the right chemical attributes, it makes it easier to interact effectively with the substrate. The dynamic region comprises of amino acids used in the chemical change accelerated by the catalytic enzyme.
Whereas not all proteins are catalytic in nature, they are dependent on molecular identification to perform their biochemical activities. Haemoglobin, which is a transport protein, should recognize the elements they carry; such as oxygen. [4, 13] On the other hand, receptors on the cell membrane should detect specific signaling compounds. Replication elements must detect specific DNA arrangements while antibodies must detect particular antigens. [12, 15]
The practical reliability of the cell is based on binding that exist between protein molecules, especially on the making of multi-protein developments.
Transmutations that result in human maladies usually interfere with protein arrangements, hence eradicating normal function. This is usually possible in the event that amino acids in a protein are shortened or radically transformed. [5] These variations alter the way protein folds and thwart the acknowledgment of binding elements.
Polymorphisms in the encrypting arrangement of the human genome can affect protein configuration. However, this is achieved by substituting one amino acid for one that has equivalent chemical properties. [11] That’s how solitary-nucleotide polymorphisms affect drug response configurations. For instance, they might create subtle transmutation to the receptor configuration with which drugs bind, understated alterations to the activity of catalysts responsible for drug metabolism.

Conclusion.

By and large, proteins play various functions in cells. The majority of proteins are involved in structural support and transport while others in enzyme reactions and interaction purposes. Certainly, just as their distinct amino acid chains as well as complex 3D structures, individual proteins have different functions.

References.

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