Structural Biochemistry/Proteins - Wikibooks, open books for an open world
Not only are these proteins assembled with different amino acid sequences, but 1: The relationship between amino acid side chains and protein conformation. From studies of the amino acid sequence and conformation of myoglobin, human α- and β-haemoglobins and lysozyme, the following conclusions have been. The term structure when used in relation to proteins, takes on a much more While the amino acid sequence makes up the primary structure of the protein, the of proteins or peptides have distinct characteristic local structural conformations.
Detailed studies then showed that nearly all the original enzymatic activity was regained if the sulfhydryl groups were oxidized under suitable conditions. All the measured physical and chemical properties of the refolded enzyme were virtually identical with those of the native enzyme.
These experiments showed that the information needed to specify the catalytically active structure of ribonuclease is contained in its amino acid sequence. Subsequent studies have established the generality of this central principle of biochemistry: The dependence of conformation on sequence is especially significant because of the intimate connection between conformation and function.
A quite different result was obtained when reduced ribonuclease was reoxidized while it was still in 8 M urea and the preparation was then dialyzed to remove the urea.
Why were the outcomes so different when reduced ribonuclease was reoxidized in the presence and absence of urea? The reason is that the wrong disulfides formed pairs in urea. There are different ways of pairing eight cysteine molecules to form four disulfides; only one of these combinations is enzymatically active. This process was driven by the decrease in free energy as the scrambled conformations were converted into the stable, native conformation of the enzyme.
The native disulfide pairings of ribonuclease thus contribute to the stabilization of the thermodynamically preferred structure. Similar refolding experiments have been performed on many other proteins.
In many cases, the native structure can be generated under suitable conditions. For other proteins, however, refolding does not proceed efficiently. In these cases, the unfolding protein molecules usually become tangled up with one another to form aggregates.
Inside cells, proteins called chaperones block such illicit interactions Sections How does an unfolded polypeptide chain acquire the form of the native protein?
These fundamental questions in biochemistry can be approached by first asking a simpler one: Examining the frequency of occurrence of particular amino acid residues in these secondary structures Table 3.
Glycine, asparagine, and proline have a propensity for being in turns. The results of studies of proteins and synthetic peptides have revealed some reasons for these preferences. Glycine readily fits into all structures and for that reason does not favor helix formation in particular. Can one predict the secondary structure of proteins by using this knowledge of the conformational preferences of amino acid residues? What stands in the way of more accurate prediction? Note that the conformational preferences of amino acid residues are not tipped all the way to one structure see Table 3.
The preference ratios of most other residues are smaller.
Indeed, some penta- and hexapeptide sequences have been found to adopt one structure in one protein and an entirely different structure in another Figure 3. Hence, some amino acid sequences do not uniquely determine secondary structure. Tertiary interactions—interactions between residues that are far apart in the sequence—may be decisive in specifying the secondary structure of some segments.
The context is often crucial in determining the conformational outcome. The conformation of a protein evolved to work in a particular environment or context. Many sequences can adopt alternative conformations in different proteins. Pathological conditions can result if a protein assumes an inappropriate conformation for the context. Striking examples are prion diseases, such as Creutzfeldt-Jacob disease, kuru, and mad cow disease.
These conditions result when a brain protein called a prion converts from its normal conformation designated PrP C to an altered one PrPSc. This conversion is self-propagating, leading to large aggregates of PrPSc.
The role of these aggregates in the generation of the pathological conditions is not yet understood. Protein Folding Is a Highly Cooperative Process As stated earlier, proteins can be denatured by heat or by chemical denaturants such as urea or guanidium chloride.
For many proteins, a comparison of the degree of unfolding as the concentration of denaturant increases has revealed a relatively sharp transition from the folded, or native, form to the unfolded, or denatured, form, suggesting that only these two conformational states are present to any significant extent Figure 3.
A similar sharp transition is observed if one starts with unfolded proteins and removes the denaturants, allowing the proteins to fold. Most proteins show a sharp transition from the folded to unfolded form on treatment with increasing concentrations of denaturants. Therefore, a solvation shell of structured water will also form to some extent around polar molecules.
Chapter 7 : The Three-Dimensional Structure of Proteins
Even though the energy of formation of an intramolecular hydrogen bond or ionic interaction between two polar groups in a macromolecule is largely canceled out by the elimination of such interactions between the same groups and water, the release of structured water when the intramolecular interaction is formed provides an entropic driving force for folding. Most of the net change in free energy that occurs when weak interactions are formed within a protein is therefore derived from the increase in entropy in the surrounding aqueous solution.
Of the different types of weak interactions, hydrophobic interactions are particularly important in stabilizing a protein conformation; the interior of a protein is generally a densely packed core of hydrophobic amino acid side chains.
It is also important that any polar or charged groups in the protein interior have suitable partners for hydrogen bonding or ionic interactions. One hydrogen bond makes only a small apparent contribution to the stability of a native structure, but the presence of a single hydrogen-bonding group without a partner in the hydrophobic core of a protein can be so destabilizing that conformations containing such a group are often thermodynamically untenable.
Chemistry of amino acids and protein structure
Most of the structural patterns outlined in this chapter reflect these two simple rules: Insoluble proteins and proteins within membranes Chapter 10 follow somewhat different rules because of their function or their environment, but weak interactions are still critical structural elements. Several types of secondary structure are particularly stable and occur widely in proteins.
Using fundamental chemical principles and a few experimental observations, Linus Pauling and Robert Corey predicted the existence of these secondary structures inseveral years before the first complete protein structure was elucidated. In considering secondary structure, it is useful to classify proteins into two major groups: Fibrous proteins play important structural roles in the anatomy and physiology of vertebrates, providing external protection, support, shape, and form.
They may constitute one-half or more of the total body protein in larger animals. Most enzymes and peptide hormones are globular proteins. Globular proteins tend to be structurally complex, often containing several types of secondary structure; fibrous proteins usually consist largely of a single type of secondary structure.
Because of this structural simplicity, certain fibrous proteins played a key role in the development of the modern understanding of protein structure and provide particularly clear examples of the relationship between structure and function; they are considered in some detail after the general discussion of secondary structure.
Each peptide bond has some double-bond character due to resonance and cannot rotate. The carbonyl oxygen has a partial negative charge and the amide nitrogen a partial positive charge, setting up a small electric dipole. Note that the oxygen and hydrogen atoms in the plane are on opposite sides of the C-N bond.
This is the trans configuration. Virtually all peptide bonds in proteins occur in thisconfiguration, although an exception is noted in Fig. The C-N bonds in the planar peptide groups shaded in bluewhich make up one-third of all the backbone bonds, are not free torotate.
Other single bonds in the backbone may also be rotationally hindered, depending on the size and charge of the R groups. Pauling and Corey began their work on protein structure in the late s by first focusing on the structure of the peptide bond. X-ray diffraction studies of crystals of amino acids and of simple dipeptides and tripeptides demonstrated that the amide C-N bond in a peptide is somewhat shorter than the C-N bond in a simple amine and that the atoms associated with the bond are coplanar.
This indicated a resonance or partial sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen Fig. The oxygen has a partial negative charge and the nitrogen a partial positive charge, setting up a small electric dipole. The four atoms of the peptide group lie in a single plane, in such a way that the oxygen atom of the carbonyl group and the hydrogen atom of the amide nitrogen are trans to each other.
From these studies Pauling and Corey concluded that the amide C-N bonds are unable to rotate freely because of their partial double-bond character. The backbone of a polypeptide chain can thus be pictured as a series of rigid planes separated by substituted methylene groups, -CH R - Fig. The rigid peptide bonds limit the number of conformations that can be assumed by a polypeptide chain. In a protein, this conformation is prohibited by steric overlap between a carbonyl oxygen and an a-amino hydrogen atom.Proteins
Figure A Ramachandran plot. The shaded areas reflect conformations that can be take up by all amino acids dark shading or all except valine and isoleucine medium shading ; the lightest shading reflects conformations that are somewhat unstable but are found in some protein structures. The Ramachandran plot in Figure shows the conformations permitted for most amino acid residues.
They also had the experimental results of William Astbury, who in the s had conducted pioneering x-ray studies of proteins. With this information and their data on the peptide bond, and with the help of precisely constructed models, Pauling and Corey set out to determine the likely conformations of protein molecules. In this structure the polypeptide backbone is tightly wound around the long axis of the molecule, and the R groups of the amino acid residues protrude outward from the helical backbone.
Protein Structure: Primary, Secondary, Tertiary, Quatemary Structures
The repeating unit is a single turn of the helix, which extends about 0. The planes of the rigid peptide bonds are parallel to the long axis of the helix.
The repeat unit is a single turn of the helix, 3. Note the positions of the R groups, represented by red spheres. These units include domains, motifs, and folds. Despite the fact that there are aboutdifferent proteins expressed in eukaryotic systems, there are many fewer different domains, structural motifs and folds.
Structural domain[ edit ] A structural domain is an element of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain.
Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the " calcium -binding domain of calmodulin ". Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimera proteins.
Structural and sequence motif[ edit ] The structural and sequence motifs refer to short segments of protein three-dimensional structure or amino acid sequence that were found in a large number of different proteins. Some of them may be also referred to as structural motifs.
Superdomain[ edit ] A superdomain consists of two or more nominally unrelated structural domains that are inherited as a single unit and occur in different proteins. The PTP-C2 superdomain evidently came into existence prior to the divergence of fungi, plants and animals is therefore likely to be about 1.
Protein folding As it is translated, polypeptides exit the ribosome as a random coil and folds into its native state. Protein denaturation may result in loss of function, and loss of native state. X-ray crystallography and calorimetry indicates that there is no general mechanism that describes the effect of temperature change on the functions and structure of proteins.
This is due to the fact that proteins do not represent a uniform class of chemical entities from an energetic point of view. The structure and stability of an individual protein depends on the ratio of its polar and non-polar residues.
They contribute to the conformational and the net enthalpies of local and non-local interactions. Taking the weak intermolecular interactions responsible for structural integrity into consideration, it is hard to predict the effects of temperature because there are too many unknown factors contributing to the hypothetical free energy balance and its temperature dependence. Internal salt linkages produce thermal stability, and whether cold temperature results in the destabilization of these linkages is unknown.