Lesson 8
Structure-Function Relationship
Just as proteins have a variety of structures, they also serve a wide variety of functions which are dictated by their structure (as well as their dynamics or movement). Proteins have roles in providing structural stability, transport, contraction (such as in muscles), sending and receiving signals, aiding in immune response, regulating gene expression, and facilitating chemical reactions. Any protein that catalyzes a chemical reaction is called an enzyme. Enzymes and non-enzymes can be either soluble or membrane proteins. Soluble proteins form a stable fold in aqueous (water) solution while membrane proteins must reside within a membrane (we will discuss membrane proteins in greater detail in the next lesson).
Enzymes
Enzymes are proteins which catalyze chemical reactions within cells. Enzymes increase the reaction rate by lowering the activation energy of the reaction (shown in the figure below). Read this excerpt from the text The Cell: A Molecular Approach (2nd ed.) to learn more about "The Central Role of Enzymes as Biological Catalysts".
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Most protein enzymes have names that end in -ase. There are many, many types of enzymes. As shown in BRENDA: The comprehensive Enzyme Information System, enzymes can be sorted into functional classes:
Oxidoreductases: catalyze oxidation and reduction reactions
Transferases: catalyze the transfer of functional groups
Hydrolases: catalyze hydrolysis reactions (splicing a molecule into two or more parts with the release of a water molecule), including proteases, nucleases, and phosphatases
Lyases: catalyze breaking bonds other than hydrolysis or oxidation
Isomerases: catalyze atomic rearrangement within a molecule
Ligases: catalyze the reaction of two molecules joining to make one
Translocases: catalyze transport of an ion or molecule across a membrane
Take a few minutes to click through these classes to see the wide array of functions enzymes serve in thousands of different organisms.
Note that all enzymes catalyze some type of reaction.
Non-Enzymes
Proteins can play many roles other than as enzymes as well. Some of these roles include (but are not limited to):
Receptors: bind a ligand and often transmit a signal
Ion channels: allow ligands, molecules, or ions to pass through a membrane
Structural proteins: provide support and structure to the cell
Motor proteins: function in movement (such as muscle contraction) by coupling ATP hydrolysis to conformational changes
Antibodies: aid in immune response by labeling foreign molecules for destruction
Hormones: aid in communication between different parts of the body
Watch this AAMC/Khan academy video about some non-enzymatic protein functions.
Protein function is dictated by structure
Protein functions are a direct result of the protein sequence and structure. As such, proteins with similar structures have a higher likelihood of having similar functions. If you have a protein sequence for which you do not know the function of you can compare it to proteins with similar sequences to make an educated guess of its function.
In order to find proteins with similar sequences (or to determine what protein a DNA or amino acid sequence codes for), you can use the BLAST (Basic Local Alignment Search Tool) database by either inputting the DNA or amino acid sequence. The results will show the protein name, what organism it is from, and the percent identity to the input sequence.
Clustal Omega is a multiple sequence alignment tool. When you input three or more sequences, it will find the best alignment between them and identify gaps
(-), identical amino acids (*), strong similarity between the amino acids (:), and weak similarity between the amino acids (.). It can also color by amino acid type if if you click "show colors".
UniProt is a database of protein sequences and functional annotations. The UniProt page for each protein gives a lot of important information such as sequence, secondary structure predictions, links to structures if there are any, function, active sites, where the protein resides in the cell, and protein domains and family.
Connecting back to the last lesson, proteins with similar sequences often have similar folds and structures. Thus, the structure of a protein (that hasn't been determined yet) can be estimated based on proteins (with determined structures) which have similar sequences. These estimated structures based on sequence similarity are called homology models. There are many different homology modeling servers, one is PHYRE2.
Assignment: Below are three protein sequences. Complete these steps to analyze the sequences.
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Put each sequence through the BLAST database to determine what protein each is and what organism it is from.
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Align the protein sequences using Clustal Omega (copy exactly as written below, with all three sequences and ># header, into the search box). What is different and/or similar about these sequences?
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Search for each protein in the UniProt database. What function do each of these proteins have? Do any have a structure determined? What protein family do they belong to? Where do they reside in the cell?
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Create a homology model of one of the protein sequences below which does not have a solved structure using PHYRE2. Analyze this model using PyMOL like we learned last week. Does this structure make sense based on what you know about its protein sequence similarity/differences observed in the sequence alignment from step 2? For example, does the protein look similar where there is similar sequences? Does it look similar where there are differing sequences? What happens were there are gaps in the sequence alignment? In PyMOL you can click Display - Sequence in order to see the amino acid sequence and if you click on an amino acid it will be highlighted on the structure. Note the number of the amino acid that the structure begins at. Does this make sense?
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Align your homology model with the known (previously determined) structure. To do this, open both structures in PyMOL. On the right hand bar for one of the proteins click A (action), align, to molecule, and click the other protein name. In the command line it will tell you the RMSD or the average distance between the two structures. Which parts of the protein align well? Which do not? Save a figure of this alignment.
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MPDVDRFGRLPWLWITVLVFVLDQVSKAFFQAELSMYQQIVVIPDLFSWTLAYNTGAAFSFLADSSGWQRWLFALIAIVVSASLVVWLKRLKKGETWLAIALALVLGGALGNLYDRMVLGHVVDFILVHWQNRWYFPAFNLADSAITVGAVMLALDMFRSKKSGEAAHG
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MPTRSLPTFLTLLLLASIDWVSKLVVLLKSCQLSPHSSAFLYSYVWGHFSFLIIPSFNEGAAFGLFAQYKIPLLIFRVCVILGLALFLRIKYKSLHRRTRIALTLILAGALGNVGDILLHGKVVDFLFLSYYSWRFPSFNLADAFISIGTLLLIGHLYFTKESKKCF
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MPDEPTGSADPLTSTEEAGGAGEPNAPAPPRRLRMLLSVAVVVLTLDIVTKVVAVQLLPPGQPVSIIGDTVTWTLVRNSGAAFSMATGYTWVLTLIATGVVVGIFWMGRRLVSPWWALGLGMILGGAMGNLVDRFFRAPGPLRGHVVDFLSVGWWPVFNVADPSVVGGAILLVILSIFGFDFDTVGRRHADGDTVGRRKADG
[1]"File:212 Enzymes-01.jpg" by OpenStax College is licensed under CC BY 3.0