The structure of a protein determines the way that it interacts with other molecules and its role in our bodies. Experimental studies of hydrophobic and hydrogen bonding variants allow us to understand protein structure and protein stability, which are both essential to the study of protein behavior.
Proteins: The Workers in Our Bodies
Scientists first became interested in protein structure in the 1930s, and since then, they have become one the most studied subjects in science (1). Proteins, which are folded peptides, make up the majority biomolecules in a cell and are responsible for many enzymatic functions such as the transportation of molecules, cell structure, DNA replication, cell division, and response to stimuli – to name just a few. This broad range of functions, compounded by many others, is the reason that protein structure is studied so closely.
Proteins are chains of amino acids, and the information for their synthesis is encoded in our genes. The sequence of amino acids in the chain of a specific protein is associated with the role each protein will play in the organism.
Forces Responsible for Protein Structure
With exception of some specific proteins, each kind of protein generally folds into a three-dimensional globular structure that is responsible for the activity it will perform within the organism (2, 3). Several forces work in unison to give proteins a specific configuration and contribute to their stability. Today’s protein analysis technology is providing groundbreaking results, allowing scientists to gain access to a more in-depth exploration of the vast world these complex macromolecules.
Hydrogen and hydrophobic interactions play very active roles in maintaining protein stability (4, 5). In hydrogen interactions, the nitrogen and oxygen atoms in the peptides form hydrogen bonds that contribute to the configuration of a protein’s three-dimensional structure (6). On the other hand, hydrophobic interactions occur once a protein folds and the non-polar amino acids in the hydrophobic interior are no longer in contact with water (7).
Other forces are also at play. In the interior of the protein there is very little space, which leads to structural enhancement from London dispersion forces, which result from the tight packing (7)*. Protein architecture can also be enhanced by disulfide bonds between two amino acids that have sulfur components. In addition, peptides can contain amino acids with negatively charged residues, such as Glutamine and Aspartate, and basic amino acids, such as Histidine, Lysine, and Arginine. This creates different regions in the proteins that have opposite charges, and attract electrostatically to each other. These forces are known as salt bridges (8).
Van del Waals forces are the least important forces in determining protein stability. They result from the attraction of transient dipoles that are formed due to the electron clouds of some of the atoms that compose the amino acids. They are weak but relevant due to their quantity.
- Mirsky AE, Pauling L. (1936) On the Structure of Native, Denatured, and Coagulated Proteins. Proc Natl Acad Sci U S A. 1936; 22:439–47.
- Uversky V. A decade and a half of protein intrinsic disorder: Biology still waits for physics. Protein Sci. 2013 Jun; 22(6): 693–724. Published online 2013 Apr 2. doi: 10.1002/pro.2261
- Wiederstein M., Gruber M., Frank K., Melo F., Sippl M. Structure-Based Characterization of Multiprotein Complexes. Structure. 2014 Jul 8; 22(7): 1063–1070. doi: 10.1016/j.str.2014.05.005
- Shirley BA, Stanssens P, Hahn U, Pace CN. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry. 1992;31:725–32.
- Pace C., Scholtz J., Grimsley G. Forces Stabilizing Proteins. FEBS Lett. 2014 Jun 27; 588(14): 2177–2184. Published online 2014 May 17. doi: 10.1016/j.febslet.2014.05.006
- Mirsky AE, Pauling L. On the Structure of Native, Denatured, and Coagulated Proteins. Proc Natl Acad Sci U S A. 1936;22:439–47.
- Lesser GJ, Rose GD. Hydrophobicity of amino acid subgroups in proteins. Proteins. 1990;8:6–13.
- Donald J., Kulp D., DeGrado W. Salt Bridges: Geometrically Specific, Designable Interactions. Proteins. 2011 Mar; 79(3): 898–915. Published online 2011 Jan 5. doi: 10.1002/prot.22927
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