Biochemistry 2.2 Protein Structure PDF

Levels of Protein StructureIntroductionWhen amino acids join into chains of two or more residues, they become peptides. Chains that contain two residues are dipeptides, those with three residues are tripeptides, and so on. Beyond about 10 residues, these chains are commonly called polypeptides. In g...

Levels of Protein StructureIntroductionWhen amino acids join into chains of two or more residues, they become peptides. Chains that contain two residues are dipeptides, those with three residues are tripeptides, and so on. Beyond about 10 residues, these chains are commonly called polypeptides. In general, polypeptides that contain more than 50 residues are called proteins.As the length of a polypeptide increases, distant residues within the peptide begin to interact with each other noncovalently (eg, through hydrogen bonds or ion-ion interactions). These interactions give rise to several levels of structure: primary, secondary, tertiary, and quaternary structure, depicted in Figure 2.10.Figure 2.10 Overview of the four levels of protein structure. Chapter 2: Peptides and Proteins482.2.01 Primary Protein StructurePrimary protein structure is described by the sequence of amino acid residues within the protein, with each residue linked to its neighbors through peptide bonds (see Figure 2.11).Figure 2.11 The primary structure of a peptide is described by its amino acid sequence and is maintained by peptide bonds between residues.The amino acid sequence of a protein is typically in the gene that corresponds to the protein (see Biology Chapter 2). Consequently, the primary structure of a protein may be changed by altering the corresponding gene through. Primary structure may also be altered by one or more peptide bonds within a protein or, less commonly, by forming new peptide bonds.Empirical measurements have shown that some amino acids are more prominent in proteins than others. Based on the observed proportions and the molecular weights of each amino acid residue, the average molecular weight of the residues in a protein has been determined to be approximately 110 Daltons (Da) or 0.11 kilodaltons (kDa) per residue (1 Da = 1 ). Using this average, the molecular weight of a protein can be used to estimate the number of amino acid residues in that protein and vice versa. Chapter 2: Peptides and Proteins49Concept Check 2.5A protein of unknown composition is measured to have a molecular mass of 60 kDa. Approximately how many amino acid residues does this protein contain?The sequence of amino acid residues in a protein determines the interactions that can form between residues. For instance, a negatively charged residue in one position may interact with a positively charged residue in a distant position, but only if the residues in between adopt a conformation that brings the two charged residues into proximity (see Figure 2.12). In aqueous solution, most proteins quickly adopt a structure that maximizes favorable interactions and minimizes unfavorable interactions between residues.Figure 2.12 Example of a peptide adopting a structure that facilitates interactions between distant, oppositely charged amino acids.In other words, the higher levels of protein structure (secondary, tertiary, and quaternary) are fully determined by the primary structure, which dictates which interactions are favorable or unfavorable. Primary structure also determines the degree of sigma bond rotation necessary to allow higher levels of structure. Consequently, in the absence of disruptive forces, a given amino acid sequence always folds into the same shape under physiological conditions. Proteins that have similar primary structures tend to have similar secondary and tertiary structures, and vice versa.2.2.02 Secondary Protein StructureSecondary protein structure arises when the functional groups of the peptide backbone interact with each other. Specifically, each interaction consists of the N−H group of one backbone group forming a with the C=O group of another backbone amide group.As discussed in Concept 2.1.02, peptide bonds do not freely rotate, and the atoms linked to the C and N in the peptide bond are all found within a single plane. Only the bonds surrounding each peptide bond can rotate. In the 1950s, Linus Pauling used these facts to predict various conformations that protein backbones might adopt within these constraints. Shortly thereafter, two of these conformations were verified to be present in many proteins. These conformations, shown in Figure 2.13, are known as the α-helix and the β-sheet. Chapter 2: Peptides and Proteins50Figure 2.13 The two most common protein secondary structures, α-helices and β-sheets, with hydrogen bonds between backbone groups shown.α-Helicesα-Helices are coils with the backbones arranged such that the N−H group of one residue\'s backbone aligns with the C=O group of a backbone that is four residues away, allowing these groups to hydrogen bond. The side chains project outward from the helix. The features and dimensions of a typical α-helix are shown in Figure 2.14. Chapter 2: Peptides and Proteins51Figure 2.14 Dimensions and backbone interactions of an α-helix.As with all secondary structures, the hydrogen bonds between backbone functional groups constitute the primary force that holds α-helices together. In addition to these backbone interactions, interactions between side chains may help further stabilize or destabilize α-helices.Most of the 20 standard amino acids are commonly found within α-helices, with the exceptions of and. The small size of glycine's side chain permits greater rotation of the residue due to decreased. In addition, this side chain is too small to have significant stabilizing interactions with other side chains in the helix. Consequently, glycine tends to make protein regions too flexible to maintain the strict features of an α-helix. causes the opposite problem: because its side chain links to the backbone at two positions instead of one, rotation of the N--Cα bond is restricted and proline is rigid. In addition, proline has no hydrogen atom bonded to its amide nitrogen, so the proline backbone nitrogen cannot hydrogen bond with a carboxyl group on another amino acid. Consequently, proline tends to cause \"kinks\" that destabilize α-helices. Chapter 2: Peptides and Proteins52Concept Check 2.6Which of the following peptide sequences would be more suitable for formation of an α-helix?A)NFEGLQDPSVB)DNLSRTIETQβ-SheetsOften called β-pleated sheets, these secondary structural elements consist of multiple amino acid strands (β-strands) that are aligned with each other. The N−H backbone groups in one strand hydrogen bond with the C=O groups of an adjacent strand, and vice versa. Adjacent β-strands may exist in one of two relative configurations: parallel or antiparallel (see Figure 2.15).Figure 2.15 Parallel and antiparallel β-strands in a β-sheet. Chapter 2: Peptides and Proteins53Antiparallel strands are arranged with the N-terminal end of one strand aligned to the C-terminal end of its neighbor. Adjacent antiparallel strands are often linked to each other by short, highly structured motifs called β-turns (see Figure 2.16). These turns consist of four amino acids arranged in a specific configuration that results in a 180-degree turn. This turn facilitates alignment of the C-terminal end of one strand with the N-terminal end of the next. β-turns commonly contain glycine and/or proline, which facilitate the sharp turn required by these structures due to glycine\'s flexibility and proline\'s ability to form cis peptide bonds.Figure 2.16 Example of a β-turn.In contrast, parallel strands are oriented such that the C-terminal ends of adjacent strands are aligned with each other, as are the N-terminal ends. Consequently, parallel strands cannot be connected by β-turns and must instead be linked by longer connections.Importantly, adjacent strands within a β-sheet do not need to consist of amino acids that are near each other in the primary structure. For instance, one strand of the sheet could be followed by flexible, unstructured regions, α-helices, or even other, separate β-sheets that eventually connect to additional strands in the β-sheet of interest. Examples of these structural features are shown in Figure 2.17. Chapter 2: Peptides and Proteins54Figure 2.17 Example of a β-sheet in which adjacent strands are not near each other in the primary structure but are brought together as the protein folds.In addition, a single β-sheet may consist of both parallel and antiparallel strands. As with α-helices, β-sheets may be further stabilized by favorable interactions between side chains, such as ionic interactions or hydrogen bonding. Chapter 2: Peptides and Proteins55Concept Check 2.7In the following image, a β-sheet containing five strands is pictured with the N- and C-terminal ends of each strand marked. The connections between strands are omitted from the image.Based on this information, what is the maximum number of β-turns that can be present in this β-sheet without altering the relative orientations of the strands?The relative amounts of α-helices and β-sheets in a protein, along with the amount of unstructured (ie, flexible loop) regions, can be measured by. For additional information on circular dichroism, see Lesson 14.4.2.2.03 Tertiary Protein StructureThe tertiary structure of a polypeptide is its three-dimensional folded form, also known as the polypeptide\'s native structure. The biological functions of proteins and polypeptides depend on their ability to interact with molecules in their surroundings. Consequently, a protein must adopt a specific shape to perform its role. In other words, a monomeric (ie, single-polypeptide) protein is functional only when folded into its correct tertiary structure.Proteins adopt their native forms by arranging themselves into the most energetically favorable configuration possible, often bringing structural elements close together that would otherwise be far apart. Chapter 2: Peptides and Proteins56For instance, an α-helix near the N-terminus may be brought into proximity with a β-sheet near the C-terminus when the protein adopts its native form (see Figure 2.18).Figure 2.18 Structural elements that are far apart in primary structure may be brought close together when a protein adopts its tertiary structure.Stabilization of Tertiary StructureThe most energetically favorable form of a protein tends to be a conformation in which are buried in the interior of the protein so that they are not exposed to water. This phenomenon, called the , is discussed in greater detail in Lesson 2.3. Due to the hydrophobic effect, the surface of a typical protein consists primarily of hydrophilic residues. These residues may interact with the water molecules in the surrounding environment, or they may interact with each other.The stability conferred on a protein by burying the hydrophobic residues is often enhanced by multiple types of noncovalent interactions between hydrophilic surface amino acid side chains. These interactions include:Hydrogen bonds between polar neutral groups (eg, threonine and glutamine)Salt bridges between oppositely charged ionic groups (eg, lysine and aspartate)Ion-dipole interactions between one ionic group and one polar neutral group (eg, arginine and serine)In addition to these noncovalent interactions, some proteins are stabilized by. Disulfide bonds are unique among the interactions that stabilize tertiary structure because they are covalent bonds. Chapter 2: Peptides and Proteins57Disulfide bonds form through of the sulfur atoms in and can be broken by reducing agents. Figure 2.19 shows various side chain interactions involved in tertiary structure.Figure 2.19 Various interactions that stabilize protein tertiary structure.In most cells, the cytosol is a highly reducing environment (ie, it contains a relatively high concentration of reducing agents) and, consequently, disulfide bonds in general do not form in cytosolic proteins. However, the lumen of the endoplasmic reticulum, the Golgi apparatus, and lysosomes, as well as the extracellular space, are all oxidizing environments. Therefore, disulfide bonds commonly form in proteins that occupy these environments (eg, ).Protein DomainsThe tertiary structure of a protein may include several distinct regions that each fold independently and often carry out different functions. These regions are known as domains. Domains are often named by their position within the protein or the characteristics that describe them.For instance, the domain closest to the N-terminus is often simply called the N-terminal domain. A domain that binds to DNA may simply be called the DNA-binding domain. As with β-sheets in secondary structure, a single domain of a protein may also include stretches of residues that are far apart in the Chapter 2: Peptides and Proteins58primary structure, which may have intervening sequences between them. An example protein with several domains is shown in Figure 2.20. Figure 2.20 Depiction of a protein containing three distinct domains.One particularly important type of domain is the transmembrane domain. Many proteins are integrated into the of a cell or organelle membrane, with some domains of the protein in contact with the cytosol and other domains in contact with the extracellular space or the lumen of the organelle. Transmembrane domains are inserted into the phospholipid bilayer and link the cytosolic domains to the other domains. A transmembrane domain may cross the membrane only once or it may cross multiple times (see Figure 2.21).Importantly, the amino acids within a transmembrane domain typically do not follow the trend of domains in aqueous environments such as the cytosol. Whereas the surface of a cytosolic domain typically contains hydrophilic residues, the surface of a transmembrane domain typically contains hydrophobic residues. The reason for this is that the surface of a transmembrane domain is not in contact with water. Instead, transmembrane domains are in contact with phospholipid tails, which are hydrophobic (see Chapter 9). Figure 2.21 Examples of transmembrane domains. Chapter 2: Peptides and Proteins59Because separate domains fold and carry out their functions independently, removal of one domain from a protein typically does not affect the folding or function of the other domains. For example, suppose the extracellular domain of a protein binds a molecule and thereby induces the cytosolic domain to catalyze a reaction. If the cytosolic domain is removed, the extracellular domain will likely still be able to bind the molecule; however, the cytosolic reaction will no longer be catalyzed.Concept Check 2.8Consider a protein containing a cytosolic domain, a transmembrane region, and an extracellular domain.For each domain, describe whether valine side chains are more likely to be found buried or on the surface of the domain.2.2.04 Quaternary Protein StructureQuaternary structure refers to interactions between several polypeptide units to form a single protein. Not all proteins have quaternary structure; many exist and function as single polypeptides. In proteins that do exhibit quaternary structure, each polypeptide is called a subunit. Each subunit is synthesized separately and, as with protein domains, subunits often begin folding into their tertiary structure independently.After synthesis and initial folding of tertiary structure, the subunits bind to each other, allowing the protein to fold into its final structure (Figure 2.22). Unlike domains, however, individual subunits often cannot function unless they are correctly interacting with the other subunits in the protein. Chapter 2: Peptides and Proteins60Figure 2.22 Quaternary structure occurs when multiple polypeptide subunits bind to each other to create one functional protein.The subunits within a protein are held together by the that stabilize tertiary structure. The interface between two subunits is often lined with hydrophobic residues, which are hidden from water when the subunits interact. In addition, side chains in one subunit may interact with side chains in another through hydrogen bonding, ion-dipole interactions, salt bridges, and (in oxidizing environments) disulfide bonds.Proteins with quaternary structure are classified by the number and types of subunits they contain (see Figure 2.23). A protein consisting of two subunits is called a dimer, a protein with three subunits is a trimer, a protein with four subunits is a tetramer, and so on. If all subunits in the protein are identical to each other, the prefix homo-- is added, whereas the prefix hetero-- is used for proteins in which at least one subunit differs from the others. For instance, a protein composed of two identical subunits is called a homodimer. In contrast, a dimer consisting of two nonidentical subunits is a heterodimer.Many proteins have more complex structures. For example, consists of four subunits total, with one pair of identical subunits called α-chains and another pair called β-chains. Each α-chain interacts with one β-chain to form a heterodimer, and the two heterodimers interact with each other to form functional hemoglobin. Therefore, hemoglobin is said to be a dimer of dimers.Some proteins are even more complex, having hundreds of subunits. Rather than denoting the exact number of subunits in these proteins they are typically called oligomers or multimers.