Sandbox Reserved 197: Difference between revisions

Line 9:

Ribonuclease A is an enzyme involved in catalyzing RNA degradation. The structure of RNase A has been determined through crystallography [http://en.wikipedia.org/wiki/Crystallography] and FABMS [http://en.wikipedia.org/wiki/Fast_atom_bombardment]. RNase A is composed of four anti-parallel B-sheets and 3 a-helixes. The <scene name='Sandbox_Reserved_197/Active_site/1'>active site</scene> lies within the cleft and houses three residues important for catalysis: His12, His119, and Lys41. Presence of eight cysteine residues that form four disulfide bonds and four ''cis'' proline residues greatly effect the structure and folding kinetics of RNase A.

== '''Folding''' ==

== '''Protein Folding''' ==

~~There~~ are ~~features~~ of ~~every protein that directly or indirectly effect the folding of that~~ protein [http://en.wikipedia.org/wiki/Protein_folding]. Several of these ~~features~~ have been identified ~~in RNase A~~ by the use of site directed mutagenesis to wildtype RNase A~~. These mutations~~ and ~~the study~~ of the ~~kinetics and final~~ structure ~~in comparison~~ to the ~~native form show whether that particular feature is involved in the folding of the protein~~.

Interatomic interactions are responsible for formation of a protein's 3D structure [http://en.wikipedia.org/wiki/Protein_folding]. Several of these interactions have been identified by the use of site directed mutagenesis to wildtype RNase A and subsequent comparison of the crystal structure to the wildtype.

==='''Proline Conformation'''===

~~One particular feature of RNase A is the~~ presence of ''cis'' proline residues. In nature, most amino acids reside in a ''trans'' conformation ~~[http://en.wikipedia.org/wiki/Cis_configuration]. Due~~ to their cyclic structure, prolines are more stable in a ''cis'' conformation. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation. The <scene name='Sandbox_Reserved_197/Tyr92-pro93/5'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. Despite a <scene name='Sandbox_Reserved_197/P93a/7'>P93A</scene> ~~mutation~~, a ''cis'' conformation still forms; this is an ~~unlikely~~ conformation for an alanine residue. Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its ~~favored~~ ''trans'' conformation~~. This points to~~ the ~~fact that this~~ ''cis'' ~~bond formation~~ is ~~a key component to~~ the ~~protein~~ structure of RNase A.

The presence of ''cis'' [http://en.wikipedia.org/wiki/Cis_configuration]proline residues plays a large role in protein folding. In nature, most amino acids reside in a ''trans'' conformation, but due to their cyclic structure, prolines are more stable in a ''cis'' conformation. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation. Importance of these conformations are demonstrated with several mutations to the wilde type.

The <scene name='Sandbox_Reserved_197/Tyr92-pro93/5'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. Despite a mutation from proline to alanine, <scene name='Sandbox_Reserved_197/P93a/7'>P93A</scene>, a ''cis'' conformation still forms; this is an unfavorable conformation for an alanine residue. Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by protein interactions other than the proline residue. Although the overall structure of RNase A is not affected by this mutation, the rate of folding greatly decreases upon insertion of the P93A mutation.

<scene name='Sandbox_Reserved_197/Cis-proline114/1'>''cis'' proline</scene>

Line 22:

Line 23:

==='''Disulfide Bonds'''===

Another important feature of the folding of RNase A is the presence of four disulfide bonds. These bonds contribute to the thermal stability and the rate of folding of RNase A. The residues involved in these linkages include <scene name='Sandbox_Reserved_197/Cys26-cys84/4'>Cys26-Cys84</scene>, <scene name='Sandbox_Reserved_197/Cys58-cys110/4'>Cys58-Cys110</scene>, <scene name='Sandbox_Reserved_197/40-95_disulfide_native_form/4'>Cys40-Cys95</scene>, and <scene name='Sandbox_Reserved_197/Cys65-cys72/5'>Cys65-Cys72</scene>. Cys26-Cys84 and Cys58-Cys110 create an interaction between an α-helix and a β-sheet. This connection is the main contributor to the thermodynamic stability. RNase A actually has a rate-determining three-disulfide intermediate. An analog of this, <scene name='Sandbox_Reserved_197/C40-95a_variant/6'>C[40,95]A</scene>, shows RNase A, missing the disulfide bond, Cys40-Cys95, that would normally occur here. As you can see in the variant, there are only 3 disulfide bonds present, shown in red.

==='''Summary'''===

==''Medical Importance''==

Sandbox Reserved 197: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 9: / Line 9: @@
 Ribonuclease A is an enzyme involved in catalyzing RNA degradation.  The structure of RNase A has been determined through crystallography [http://en.wikipedia.org/wiki/Crystallography] and FABMS [http://en.wikipedia.org/wiki/Fast_atom_bombardment].  RNase A is composed of four anti-parallel B-sheets and 3 a-helixes. The <scene name='Sandbox_Reserved_197/Active_site/1'>active site</scene> lies within the cleft and houses three residues important for catalysis: His12, His119, and Lys41. Presence of eight cysteine residues that form four disulfide bonds and four ''cis'' proline residues greatly effect the structure and folding kinetics of RNase A.
-== '''Folding''' ==
+== '''Protein Folding''' ==
-There are features of every protein that directly or indirectly effect the folding of that protein [http://en.wikipedia.org/wiki/Protein_folding].  Several of these features have been identified in RNase A by the use of site directed mutagenesis to wildtype RNase A.  These mutations and the study of the kinetics and final structure in comparison to the native form show whether that particular feature is involved in the folding of the protein.
+Interatomic interactions are responsible for formation of a protein's 3D structure [http://en.wikipedia.org/wiki/Protein_folding].  Several of these interactions have been identified by the use of site directed mutagenesis to wildtype RNase A and subsequent comparison of the crystal structure to the wildtype.
 ==='''Proline Conformation'''===
-One particular feature of RNase A is the presence of ''cis'' proline residues.  In nature, most amino acids reside in a ''trans'' conformation [http://en.wikipedia.org/wiki/Cis_configuration]. Due to their cyclic structure, prolines are more stable in a ''cis'' conformation. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation. The <scene name='Sandbox_Reserved_197/Tyr92-pro93/5'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. Despite a <scene name='Sandbox_Reserved_197/P93a/7'>P93A</scene> mutation, a ''cis'' conformation still forms; this is an unlikely conformation for an alanine residue.   Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its favored ''trans'' conformation. This points to the fact that this ''cis'' bond formation is a key component to the protein structure of RNase A.
+The presence of ''cis'' [http://en.wikipedia.org/wiki/Cis_configuration]proline residues plays a large role in protein folding.  In nature, most amino acids reside in a ''trans'' conformation, but due to their cyclic structure, prolines are more stable in a ''cis'' conformation. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation. Importance of these conformations are demonstrated with several mutations to the wilde type.
+The <scene name='Sandbox_Reserved_197/Tyr92-pro93/5'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. Despite a mutation from proline to alanine, <scene name='Sandbox_Reserved_197/P93a/7'>P93A</scene>, a ''cis'' conformation still forms; this is an unfavorable conformation for an alanine residue.   Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by protein interactions other than the proline residue. Although the overall structure of RNase A is not affected by this mutation, the rate of folding greatly decreases upon insertion of the P93A mutation.
 <scene name='Sandbox_Reserved_197/Cis-proline114/1'>''cis'' proline</scene>
@@ Line 22: / Line 23: @@
 ==='''Disulfide Bonds'''===
 Another important feature of the folding of RNase A is the presence of four disulfide bonds.  These bonds contribute to the thermal stability and the rate of folding of RNase A.  The residues involved in these linkages include <scene name='Sandbox_Reserved_197/Cys26-cys84/4'>Cys26-Cys84</scene>, <scene name='Sandbox_Reserved_197/Cys58-cys110/4'>Cys58-Cys110</scene>, <scene name='Sandbox_Reserved_197/40-95_disulfide_native_form/4'>Cys40-Cys95</scene>, and <scene name='Sandbox_Reserved_197/Cys65-cys72/5'>Cys65-Cys72</scene>.  Cys26-Cys84 and Cys58-Cys110 create an interaction between an α-helix and a β-sheet.  This connection is the main contributor to the thermodynamic stability.  RNase A actually has a rate-determining three-disulfide intermediate.  An analog of this, <scene name='Sandbox_Reserved_197/C40-95a_variant/6'>C[40,95]A</scene>, shows RNase A, missing the disulfide bond, Cys40-Cys95, that would normally occur here.  As you can see in the variant, there are only 3 disulfide bonds present, shown in red.
+==='''Summary'''===
 ==''Medical Importance''==