User:R. Jeremy Johnson/Oligomers

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Oligomers of Bovine Ribonuclease A

Introduction

RNase A minor dimer, 1a2w
RNase A minor dimer, 1a2w

Bovine pancreatic ribonuclease A (RNase A) is an enzyme that catalyzes the hydrolysis of RNA through acid-base catalysis. RNase A has the capability to structurally form dimers, trimers, tetramers, and pentamers based on the structure of the RNase A monomer. Though there are many oligomers, the three-dimensional structure for only the major dimer, minor dimer, and minor trimer are known. Unlike the monomers, all the oligomers are capable of catalyzing the hydrolysis of double stranded RNA (dsRNA).[1] The oligomers are formed by 3D domain swapping, which can occur once or twice per monomeric unit [2]. The 3D domain swapping has no impact on the formation of active sites which is the same in the monomers and all oligomers.[2] The oligomers of RNase A also show medical relevance as antitumor drugs as models to understand the possible cause of Alzheimer's.

Dimers

Ribonuclease A Minor Dimer

Ribonuclease A has both a and dimer which are very similar to one another. Though they are similar, they are formed by different types of 3D domain swapping. 3D domain swapping occurs when identical domains are interchanged. The major dimer is formed by 3D domain swapping the β-strand of the C-terminus.[3] The minor dimer, on the other hand, is formed by 3D domain swapping of the α-helix on the N-terminus [3]. Domain swapping is extremely specific and can only occur at the or the .


Both dimers conserve the structure of the two monomers except for the conformation at the hinge loops. The is the location where the two monomers connect acting like the hinge of a door.[2] The most important component of the hinge loops is Ala19. gives these hinges their flexibility. This flexibility allows the dimers to adopt different orientations.[3]


Not only is the structure of the monomers conserved in the dimers, but the active is also conserved. [3] The of both dimers contains His12, Lys41, and His119 residues. The active sites are a composite of the monomer subunits containing from one monomer and His119 form the other monomer.[2] During domain swapping, the active site is not disturbed, so the dimers are able to retain their enzymatic activity.


Trimers

RNase A trimers are formed in the same way as the dimers, except there are now three monomeric subunits. There is both a major and minor trimer. The structure of the major trimer is not known, but the two trimers can be separated by both chromatography and gel electrophoresis. [4] The major trimer is more common than the minor trimer.

Minor Trimer of RNase A

The forms a cyclic propeller like shape. It is 3D domain swapped at the C-terminus of the beta strand.[4] No domain swapping a the N-terminus has been seen. When the minor trimer dissociates, it forms a dimer and a monomer. The minor and major dimer are both formed, but the major dimer is much more common.[4]


Similar to the dimer, the structure of the monomer is conserved except for the . The of the trimers are made up of the same amino acid residues as the monomers and dimers. The trimer's active site is slightly different from that of the monomer and dimer because it has a trap.[4] A total of four sulfate ions bind to the minor trimer, three to the active sites, and one to the hinge loop. residues from each subunit as well as other amino acid residues bind to the sulfate ion. An intricate network of hydrogen bonding holds the sulfate ion in the trap. [4] The monomers and dimers also have sulfate ions bond to their active site, but the ions seem to have a stronger presence within the trimer. The ions are bound to the active site are completely surrounded by water, light blue spheres, which is responsible for the to the sulfate ion.


Enzymatic Activity

The monomers, dimers, and trimers all have significant enzymatic activity. The higher the order of the oligomer, the higher its enzymatic activity.[4] The pentamers, though their structure is not known, have shown the highest enzymatic activity. Though the higher order oligomers are better enzymes, they are also degraded into their subunits faster.[1]


The higher activity toward dsRNA is related to shorter distances between active sites. The higher ordered oligomers are typically more tightly packed which would decrease the distance between active sites, and make them more active.[4] For example, the major dimer is more active than the minor dimer, while the minor trimer is more active than the major trimer.[4] Liu et. al. also predicts that the twisted orientation of the dimers and trimers allows for the destabilization of dsRNA. Because the monomer does not have a twisted structure, it is not able to destabilize dsRNA.[4]

Medical Relevance

Alzheimer’s disease is a terminal disease that slowly degenerates the brain. One of the possible causes of Alzheimer’s is amyloid deposits throughout the brain. Though RNase A oligomers are not the amyloid deposits that cause Alzheimer’s, the folding of these oligomers gives clues about the formation of the amyloid deposits responsible for Alzheimer’s.


The 3D domain swapping has many similarities with the formation of amyloid fibers. Both are highly specific reactions coming from only one type of monomer and these reactions can form linear aggregates. [4] These aggregates of proteins are formed by hydrogen bonding at the hinge loops which form an antiparallel β-pleated sheet. [4] This most commonly happens with the major dimer. Liu suggests that all proteins are capable of forming aggregates by domain swapping as long as they are in high concentration and partially destabilized. [4] Forty different proteins who form oligomers by 3D domain swapping have already been identified.[5] As 3D domain swapping becomes more understood, it will offer insight to the amyloid formation in Alzheimer’s patients.


The RNase A 3D domain swapped oligomers show significant biological activity including allostery, antitumor, and immunosupressive activity. In antitumor activity, the oligomers degrade dsRNA, but they are also capable of degrading DNA and RNA hybrids which can be found during the translation of genes.[1] This same activity has not been observed in the monomer and the non-3D domain swapped oligomers .[3] This could be due to the fact that the monomer has a cystolic RNase A inhibitor that is unable to inhibit the active sites of the oligomers. [4]


All oligomers of RNase A have antitumor activity, but the higher ordered oligomers show greater activity. [1] Though the higher ordered oligomers are more active, they are also much more unstable in vivo, and the pathway inside the cell is unknown. Before oligomers can be used as an antitumor drug and to prevent the degradation of dsRNA in healthy cells, the pathway of high ordered oligomers into the cell needs to be monitored, as well as their function within the cell.

References

  1. 1.0 1.1 1.2 1.3 Matousek J, Gotte G, Pouckova P, Soucek J, Slavik T, Vottariello F, Libonati M. Antitumor activity and other biological actions of oligomers of ribonuclease A. J Biol Chem. 2003 Jun 27;278(26):23817-22. Epub 2003 Apr 14. PMID:12697760 doi:10.1074/jbc.M302711200
  2. 2.0 2.1 2.2 2.3 Liu Y, Gotte G, Libonati M, Eisenberg D. A domain-swapped RNase A dimer with implications for amyloid formation. Nat Struct Biol. 2001 Mar;8(3):211-4. PMID:11224563 doi:10.1038/84941
  3. 3.0 3.1 3.2 3.3 3.4 Liu Y, Hart PJ, Schlunegger MP, Eisenberg D. The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3437-42. PMID:9520384
  4. 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 Liu Y, Gotte G, Libonati M, Eisenberg D. Structures of the two 3D domain-swapped RNase A trimers. Protein Sci. 2002 Feb;11(2):371-80. PMID:11790847
  5. Libonati M, Gotte G. Oligomerization of bovine ribonuclease A: structural and functional features of its multimers. Biochem J. 2004 Jun 1;380(Pt 2):311-27. PMID:15104538 doi:10.1042/BJ20031922

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R. Jeremy Johnson, Jaime Prilusky

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