Search results
The spike protein of SARS-CoV-2 appears to promote rapid viral spread by replacing aspartic acid (D) at position 614 with glycine (G) in the carboxy(C)-terminal region of the S1 domain. The D614G mutation is possibly one of the best examples of the efects of mutational alterations in the SARS-CoV-2 spike protein.
The crystallographic structure of RBD of Spike protein was downloaded from PDB ID: 6LZG and ACE2 receptor was removed from the complex, and the Spike protein was minimized using AutoDockTools. The authors used the AutoDock Vina version 1.1.2 to run the docking simulations and the blind docking to confirm the biding site at ACE2–S-protein interaction region.
- Goal
- After this chapter, you should be able to
- Proteins have diverse functions
- a wide range of three-dimensional structures
- DNA double helix p53 protein
- The sequence of amino acids in a protein determines its folded structure
- Box 1 Sickle-cell disease: one amino acid makes a diference
- Sickled red blood cell
- Peptide bonds are flat, polar, and not free to rotate
- Box 2 Hybrid orbitals
- O N
- Peptide bonds favor the trans configuration
- Phenylalanine, tyrosine, and tryptophan contain aromatic rings
- Amino acid side chains afect the conformation of the peptide backbone
- Cysteine side chains can form non-peptidic bonds in proteins
- Amino acids often function cooperatively in proteins
- Summary
- H3N H2 O N N O H2 O O O O
To understand how common and dissimilar features of amino acids determine the chemical and physical properties of proteins.
explain why peptide bonds are polar and prefer the trans configuration. explain how side chains confer distinct chemical and physical properties on amino acids. draw a peptide of a given sequence at a specified pH. Many of the most important macromolecules in living systems are polymers. These polymers are composed of small building blocks that are...
Owing to their enormous diversity, cells employ proteins to perform numerous tasks (Figure 3). Some proteins function as enzymes, which catalyze chemical reactions by reducing ΔG‡. Nearly all enzymes are proteins, and as we saw in the previous chapter, cells are able to carry Figure 1 Polymers are macromolecules composed of small-molecule monomers ...
Shown is an X-ray crystal structure of the p53 protein bound to a DNA double helix. DNA adopts a predictable double-helix structure, regardless of its sequence. The structures of proteins, however, vary widely depending on the specific sequence of amino acids of which they are composed. proteins like actin and tubulin are often used as scafolds t...
beam of X-rays penetrates through the crystal lattice. Some of the X-rays are difracted as they encounter the individual atoms that make up the molecules in the crystal lattice. The difraction creates a characteristic pattern of reflections that is collected on an X-ray film and from which the arrangement of atoms can be reconstructed. This techniq...
The specific order of amino acids in a protein is known as its primary structure. It is this sequence that determines the three-dimensional architecture of a protein. A famous experiment that proves that all the information necessary for proper folding of a protein is contained in its primary structure is presented in the next chapter.
You might imagine that changing a single amino acid in a protein consisting of a hundred or more amino acids would have little efect on the protein’s folded shape or function. Often this is the case, but sometimes a single change makes a profound diference. Figure 5 shows one example in which the substitution of a single amino acid significantly al...
Figure 5 Sickle-cell disease is caused by a single amino acid change in the hemoglobin protein (A) Line drawings of a portion of the hemoglobin (left) and sickle-cell hemoglobin (right) proteins. Normal hemoglobin contains the amino acid glutamate at position 6 in the primary sequence. In individuals with sickle-cell disease, this glutamate is r...
The chemical properties of the peptide bond are important for determining the shape of the polypeptide chain. Some of the bonds of the peptide chain are free to rotate, but the peptide bond itself can only adopt certain conformations. To understand why, we return to the topic of the orbitals that surround atoms. When a covalent bond forms, the orbi...
As we have seen, ethylene is unable to rotate around its double bond due to its π bond. Another feature of ethylene is that its hydrogen and carbon atoms are in a planar configuration; they have a trigonal planar geometry. This means that the atomic orbitals linking the hydrogen and carbon atoms are pointing to the vertices of a triangle. The signi...
Bond is free to rotate R4 Bond is not free to rotate; peptide bond The peptide bond con nes six atoms to the same plane Sets of coplanar atoms can rotate relative to one another = O H N O OH O H N N H O O Figure 13 The peptide bond is flat and not free to rotate (A) Diagram of a generic polypeptide chain. Colored rectangles indicate ...
Because the peptide bond is not able to rotate freely, it can exist in two possible configurations known as geometric isomers. To understand the concept of geometric isomers, let us first consider the simple case of the hypothetical molecule shown in Figure 16A. It can exist as two geometric isomers referred to as cis and trans, which describe how ...
The aromatic amino acids—phenylalanine, tyrosine, and tryptophan—are unique in that they contain rings with alternating double bonds. Actually, the double bonds in these rings are not fixed. Rather, the electrons are delocalized among all the carbon atoms due to resonance. Aromaticity imparts properties that are exploited both in nature and in the ...
As we mentioned earlier, the side chains in a polypeptide chain determine how it folds into a three-dimensional structure. This occurs in part because the amino acid side chains difer in their size and flexibility, which in turn biases the peptide backbone toward certain conformations. Some amino acids have large, bulky side chains (e.g., phenylala...
The amino acid cysteine contains a sulfhydryl (-SH) group on its side chain. Sulfhydryls can be oxidized to form disulfide bonds in which two cysteine side chains, often from distant locations in the primary sequence, come together to form a sulfur-sulfur covalent bond (Figure 18). The formation of such disulfide bonds in proteins rigidifies the pr...
The amino acid side chains we have been describing are key functional components of proteins. Many proteins have enzymatic functions, and in these cases the side chains are directly involved in the reactions the enzymes catalyze. One class of enzymes, proteases, has evolved to catalyze the breakdown of peptide bonds in proteins. Many proteases cont...
Proteins are the most diverse and versatile macromolecules found in living systems. Proteins are polymeric chains of amino acid monomers connected by covalent peptide bonds. Unlike most other biological polymers, proteins fold into unique structures with distinct physical and chemical properties. As a result, cells use proteins for a broad range of...
The amide functional group found in the peptide backbone cannot be ionized. This structure would be correct if the circled nitro-
- 9MB
- 24
Oct 5, 2021 · SARS-CoV-2 encodes at least 12 canonical open reading frames in its ~29.9 kilobase RNA genome 1, 2. Viral RNA is initially translated into two polyproteins with subsequent expression of multiple ...
- Jeffrey M. Schaub, Chia Wei Chou, Hung Che Kuo, Kamyab Javanmardi, Ching Lin Hsieh, Jory Goldsmith, ...
- 2021
The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein ...
spike proteins, camouflaging them from our immune system as they enter the body. Vaccines Many vaccines for COVID-19 depend on the spike protein. For example, the Novavax vaccine uses nanoparticles made up of spike proteins. From February 2020, studies identified structures of the SARS-CoV-2 spike protein using electron microscopy. Scientists ...
People also ask
What is a spike protein?
What techniques are used in spike protein research?
What recombination causes 2 spike protein?
Which peptide interacts majoritarian with spike protein?
How does a virus cleave a spike protein?
How does Spike mediate host cell entry?
SARS-CoV-2 spike (S) glycoprotein is the key target of current vaccine development efforts to combat COVID-19; neutralizing antibodies bind S and interfere with S binding to its receptor ...
