Sandbox Reserved 197: Difference between revisions

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== '''Introduction''' ==

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.

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 β-sheets and 3 α-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.

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

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==='''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.

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 stabilize an interaction between an α-helix and a β-sheet. This connection is the main contributor to the thermodynamic stability.

Measurements of protein activity upon removal of disulfide bridges show that the active center is very small and not all disulfide bridges are essential for reactivity of the protein. However, removal of disulfide bonds destabilizes the hydrophobic core and decreases the rate of folding. 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 and the 2D structure, there are only 3 disulfide bonds present, shown in red.

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

Protein folding is not due to one interaction, but a network of interactions within the protien. When a proline or disulfide bond is removed, the structural changes are usually confined to the site of mutation and minor structural changes occur within close proximity to the mutation. Mutation of a ''cis'' proline is usually accompanied by an insertion or deletion in order to provide more flexibility for the structure. Although the effects of mutations seem to be localized, replacing proteins greatly effects the stability of the molecule and the rate of folding.

==''Medical Importance''==

Protein folding~~, along with its inhibitions, is immensely important to the human~~. ~~Such diseases~~ as ALS, Alzheimer's Disease, and Parkinson's Disease can all be traced back to ~~the~~ protein~~. Proteins~~ can form aberrant aggregates when they do not fold correctly. This abnormaility can be fatally toxic to ~~the~~ human nerve cells. During folding, proteins sometimes make a mistake. Each protein contains <scene name='Sandbox_Reserved_197/Hydrophobic-hydrophilic/1'>hydrophobic and hydrophilic residues</scene>. The hydrophilic residues lie on the outer part of the protein and the hydrophobic residues bury themselves due to the hydrophobic effect [http://en.wikipedia.org/wiki/Hydrophobic_effect]. In the case of these aggregates, the mistake exposes "sticky" <scene name='Sandbox_Reserved_197/Hydrophobic/1'>hydrophobic patches</scene> of the interior that can cause several proteins to stick to one another. In the future researchers hope to design drugs that combat ~~this mistake~~ in ~~the~~ protein folding. The use of ribonuclease A in protein folding research has been an instrumental feature in designing experiments to determine these "misfolding" snapshots and in developing therapies to prevent this problem in the future.

Protein folding has several medical implications. Diseases such as ALS, Alzheimer's Disease, and Parkinson's Disease can all be traced back to protein folding because proteins can form aberrant aggregates when they do not fold correctly. This abnormaility can be fatally toxic to human nerve cells. During folding, proteins sometimes make a mistake. Each protein contains <scene name='Sandbox_Reserved_197/Hydrophobic-hydrophilic/1'>hydrophobic and hydrophilic residues</scene>. The hydrophilic residues lie on the outer part of the protein and the hydrophobic residues bury themselves due to the hydrophobic effect [http://en.wikipedia.org/wiki/Hydrophobic_effect]. In the case of these aggregates, the mistake exposes "sticky" <scene name='Sandbox_Reserved_197/Hydrophobic/1'>hydrophobic patches</scene> of the interior that can cause several proteins to stick to one another. In the future researchers hope to design drugs that combat mistakes in protein folding. The use of ribonuclease A in protein folding research has been an instrumental feature in designing experiments to determine these "misfolding" snapshots and in developing therapies to prevent this problem in the future.

=='''References'''==

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@@ Line 7: / Line 7: @@
 == '''Introduction''' ==
-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.
+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 β-sheets and 3 α-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.
 == '''Protein Folding''' ==
@@ Line 21: / Line 21: @@
 ==='''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.
+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 stabilize an interaction between an α-helix and a β-sheet.  This connection is the main contributor to the thermodynamic stability.
+Measurements of protein activity upon removal of disulfide bridges show that the active center is very small and not all disulfide bridges are essential for reactivity of the protein. However, removal of disulfide bonds destabilizes the hydrophobic core and decreases the rate of folding. 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 and the 2D structure, there are only 3 disulfide bonds present, shown in red.
 ==='''Summary'''===
+Protein folding is not due to one interaction, but a network of interactions within the protien. When a proline or disulfide bond is removed, the structural changes are usually confined to the site of mutation and minor structural changes occur within close proximity to the mutation. Mutation of a ''cis'' proline is usually accompanied by an insertion or deletion in order to provide more flexibility for the structure. Although the effects of mutations seem to be localized, replacing proteins greatly effects the stability of the molecule and the rate of folding.
 ==''Medical Importance''==
-Protein folding, along with its inhibitions, is immensely important to the human.  Such diseases as ALS, Alzheimer's Disease, and Parkinson's Disease can all be traced back to the protein.  Proteins can form aberrant aggregates when they do not fold correctly.  This abnormaility can be fatally toxic to the human nerve cells.  During folding, proteins sometimes make a mistake.  Each protein contains <scene name='Sandbox_Reserved_197/Hydrophobic-hydrophilic/1'>hydrophobic and hydrophilic residues</scene>.  The hydrophilic residues lie on the outer part of the protein and the hydrophobic residues bury themselves due to the hydrophobic effect [http://en.wikipedia.org/wiki/Hydrophobic_effect]. In the case of these aggregates, the mistake exposes "sticky" <scene name='Sandbox_Reserved_197/Hydrophobic/1'>hydrophobic patches</scene> of the interior that can cause several proteins to stick to one another.  In the future researchers hope to design drugs that combat this mistake in the protein folding.  The use of ribonuclease A in protein folding research has been an instrumental feature in designing experiments to determine these "misfolding" snapshots and in developing therapies to prevent this problem in the future.
+Protein folding has several medical implications. Diseases such as ALS, Alzheimer's Disease, and Parkinson's Disease can all be traced back to protein folding because proteins can form aberrant aggregates when they do not fold correctly.  This abnormaility can be fatally toxic to human nerve cells.  During folding, proteins sometimes make a mistake.  Each protein contains <scene name='Sandbox_Reserved_197/Hydrophobic-hydrophilic/1'>hydrophobic and hydrophilic residues</scene>.  The hydrophilic residues lie on the outer part of the protein and the hydrophobic residues bury themselves due to the hydrophobic effect [http://en.wikipedia.org/wiki/Hydrophobic_effect]. In the case of these aggregates, the mistake exposes "sticky" <scene name='Sandbox_Reserved_197/Hydrophobic/1'>hydrophobic patches</scene> of the interior that can cause several proteins to stick to one another.  In the future researchers hope to design drugs that combat mistakes in protein folding.  The use of ribonuclease A in protein folding research has been an instrumental feature in designing experiments to determine these "misfolding" snapshots and in developing therapies to prevent this problem in the future.
 =='''References'''==