An Introduction to Protein Structure
An Introduction to Protein Structure
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Courses
Mike Levitts protein structure course:
Russ Altman's Algorithm Course
Van der Waals
Proteins are more flexible than nucleic acids in structure because of both the larger number of types of residues and the increased flexibility and lower charge density of the polypeptide backbone. Proteins can serve many roles in the cell; as enzymes, as structural components, membrane components, as templates, as substrates and as products of reactions. Many aspects of protein metabolism are catalyzed and regulated by the cell. These include their rates of expression, their translation, their folding, their targeting to the proper cellular location and their degradation. Proteins, and the functions they catalyze, are the end-product of the genes that encode them. Some of the most important functions of proteins are to regulate the expression of other proteins.
In this lecture we will discuss the components of proteins, their covalent structure, their non-covalent interactions, higher order structures such as motifs and domains and then give several examples of different types of protein folds. It will be extremely useful for you to down load the Kinemage 4.2 program and the Proteach Kinemage collection for reviewing the material presented in the class. Pointers to the locations to obtain this program and the Proteach files are on the course Web page.
The amino acid residues of proteins are defined by an amino group and a carboxyl group connected to an alpha carbon to which is attached a hydrogen and a side chain group R. The smallest amino acid, glycine, has a hydrogen atom in place of a side chain. All other amino acids have distinctive R groups. Because the alpha carbon of the other amino acids have four different constituents, the alpha carbon atom is an asymmetric center and most naturally occurring amino acids are in the L form.
Amino acids fall into several naturally occurring groups including hydrophobic, hydrophilic, charged, basic, acidic, polar but uncharged, small polar, small hydrophobic, large hydrophobic, aromatic, beta-branched, sulfur containing etc. Hydrophobic amino acids, sometimes called non-polar amino acids, reside primarily on the interior of the protein. Hydrophilic amino acids, sometimes called polar amino acids, reside primarily on the exterior of the protein. Many amino acids will fall into more than one group since each amino acid side chain has several properties.
Amino acids are linked to each other by peptide bonds. Peptide bonds are formed by the dehydration of the carboxyl group of one amino acid and the amino group of the next. Because of the resonance structure of the electron orbitals on the amino and carboxyl groups, the peptide bond is planar. The dihedral angle between the amino group and the alpha carbon and the alpha carbon and the carboxyl group are free to rotate and these angles are referred to as the phi-psi angles. Glycine, with the smallest side chain, has the most conformational flexibility about the phi-psi angles. Other amino acids are restricted in their rotation due to steric hindrance from the side chains. The rotation of the dihedral angles of side chains about the different bonds, referred to as chi-1, chi-2 etc., are also restricted for different side chain elements. Proline, which in which the side chain is linked back to the backbone is the most restricted; only two conformations are permitted.
Forces determining protein structure
Several covalent and non-covalent forces determine protein structure. The list of forces include (not exhaustive):
1) van der Waals interactions between immediately adjacent atoms: These non-covalent forces result from the attraction of one atoms nucleus for the electrons of another atom in a non-covalent form (no sharing of orbitals). These forces are much weaker than covalent interactions and the interaction distances are much longer than covalent bonds and much shorter than the other non-covalent interactions. Van der Waals interactions occur at distances between 3 and 4 Å. They are very weak beyond 5Å and electron repulsion prevents atoms from getting much closer than 3Å. Van der Waals interactions are non-directional and very weak. However, significant energy of stabilization can be obtained in the central hydrophobic core of proteins by the additive effect of many such interactions.2) Hydrophobic force: The hydrophobic force is really a negative non-covalent force. The presence of hydrophobic side chains in aqueous solution induces the formation of structured water (clathrate cages of water molecule form, like miniature ice crystals about the hydrophobic side chains). This reduction in entropy of the water molecules is a very unfavorable resulting in a strong force to keep hydrophobic side chains buried in the interior of the protein. The hydrophobic force is one of the largest determinants of protein structure. Most secondary structural elements we will discuss have an amphipathic nature, one hydrophobic side and one hydrophilic side because the structure lies on the surface of the protein.
3) Electrostatic forces: The attraction of oppositely charged side chains can form salt-bridges that stabilize secondary and tertiary structures. The electrostatic force is quite strong, falling off as the square of the distance between the charged atoms. It also depends heavily on the dielectric constant of the medium in which the protein is dissolved. It is strongest in a vacuum and 80 fold weaker in water and weaker still at elevated salt solutions. Water and ions can shield electrostatic interactions reducing both their strength and distance over which they operate.
4) Dipole moments. Dipole moments are caused by pairs of charges separated by a larger distance than permitting a salt- or ion bridge. The dipole moment gives rise to an electric field along the entire length of a structural element. Dipole moments are often used by proteins to attract and position charged substrates and products. The peptide chain naturally has a dipole moment because the N-terminus carries about 1/2 a positive charge and the C-terminus carries about 1/2 unit of negative charge. The alpha helix is known to carry a partial negative charge at its C-terminus and a positive charge at its N-terminus. In order to help neutralize this charge distribution, alpha helices often have acidic residues near their N-terminus and a basic residue near their C-terminus.
5) Hydrogen bonds: Hydrogen bonds occur when a pair of nucleophilic atoms such as oxygen and nitrogen share a hydrogen between them. The hydrogen may be covalently attached to either nucleophilic atom (the H-bond donor) and shared with the other atom (the H-bond receptor). H-bonds are directional and their strength deteriorates dramatically as the angle changes. Hydrogen bonds do not, in general, contribute to the net stabilization energy of proteins because the same groups that hydrogen bond to each other in a native protein structure, can hydrogen bond to water in the denatured state. However, hydrogen bonds are extremely important because of their directionality, they can control and limit the geometry of the interactions between side-chains. This is shown most dramatically in patterns of hydrogen bonding between the carboxyl groups and the amino groups in the peptide backbone that give rise to alpha helix and beta strand conformations.
6) Covalent bond distances and torsion angles: The major properties of the covalent bonds hold proteins together are their bond distances and bond angles. In particular, the bond angles between two adjacent bonds on either side of a single atom, or the dihedral angles between three contiguous bonds and two atoms control the geometry of the protein folding. The preferred dihedral angles for different secondary structural elements are discussed below.
Preferred secondary structures
Alpha helices are the most well known element of protein structure, proposed by Pauling and confirmed in the first structure determined, myoglobin, alpha-helices have distinctive patterns of hydrogen bonding and phi-psi angles. They are generally between 5 and 20 residues in length, but some proteins and coiled-coil structures can be considerably longer. The carboxyl groups of the backbone hydrogen bond to the amino group of a residue four amino acids distant along the chain. Alpha helices generally have a pitch of about 3.5 residues per turn, but there are forms of helices with tighter (3 residues per turn) and longer (4 residues per turn).
Alpha helices can be coiled about them selves in both two coil, three coil and four coil (four helix bundle) conformations. Alpha helices can exist internal in proteins (generally hydrophobic), on the surface of proteins (amphipathic) or in membranes (hydrophobic). Alpha helices can span membranes either singly or in groups.
Beta-strands are an extended form in which the side chains alternate on either side of the extended chain. The backbones of beta-strands hydrogen bond with the backbone of an adjacent beta strand to form a beta-sheet structure. The strands in a beta sheet can be either parallel or anti-parallel and the hydrogen-bonding pattern is different between the two forms. Anti-parallel beta stands are often linked by short loops containing 3-5 residues in highly characteristic conformations. Longer loops are occasionally found where the loop plays an important role in substrate binding or an active site. The antigen-combining site of the immunoglobulins is an important example of this.
Beta sheets can be internal to a protein (largely hydrophobic) or on the surface in which case they are amphipathic, with every other amino acid side chain alternating between hydrophobic and hydrophilic nature.
The peptide backbone is constrained by steric hindrance, and hydrogen bonding patterns that limit its torsional angles (phi-psi angles) to certain limits. Plots of phi versus psi dihedral angles for amino acid residues are called Ramachandran plots. One can tell if the backbone is following a helical or a an extended beta strand structure based on the values of the phi-psi angles over a length of backbone (usually 3-4 residues is sufficient).
Branden, C. & Tooze, J. Introduction to Protein Structure, Second Edition, Garland Publishing, New York.
Creighton, T. E. (1993). Proteins: Structures and Molecular Properties. (Second Edition ed.). New York: Freeman.
Creighton, T. E. (Ed.). (1992). Protein Folding. New York: W. H. Freeman & Co.
Darby, N. J., & Creighton, T. E. (1993). Protein Structure. Oxford: IRL Press.
Schulz, G. E., & Schirmer, R. H. (1985). Principles of Protein Structure. New York: Springer-Verlag.
Stryer, L. (1995). Biochemistry. (Fourth Edition ed.). New York: W. H. Freeman & Co.
