User:R. Jeremy Johnson/Folding Synthesis: Difference between revisions

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

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 the ''cis'' conformation than any other amino acid. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation.<ref name="Lehninger" /> The importance of these conformations are demonstrated based on the structure of RNase A variants with several mutations to the wild type amino acid sequence.

Located in an outer <scene name='Sandbox_Reserved_197/Tyr92-pro93_loop/3'>loop</scene> of RNase A, the <scene name='Sandbox_Reserved_197/Tyr92-pro93/7' target='0'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. When proline was mutated to alanine, <scene name='Sandbox_Reserved_197/P93a/9' target='0'>P93A</scene>, a ''cis'' conformation still forms at position 93 which is an energetically unfavorable conformation for an alanine residue <ref name ='1'>PMID:9605332</ref>. Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by other interactions within the folded protein structure. 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, suggesting an important kinetic contribution of ''cis'' prolines to protein folding.<ref name="1" />

Located in an outer <scene name='Sandbox_Reserved_197/Tyr92-pro93_loop/3'>loop</scene> of RNase A, the <scene name='Sandbox_Reserved_197/Tyr92-pro93/7' target='0'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. When proline was mutated to alanine, <scene name='Sandbox_Reserved_197/P93a/9' target='0'>P93A</scene>, a ''cis'' conformation still forms at position 93 which is an energetically unfavorable conformation for an alanine residue <ref name ='Tyr92'>PMID:9605332</ref>. Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by other interactions within the folded protein structure. 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, suggesting an important kinetic contribution of ''cis'' prolines to protein folding.<ref name="Tyr92" />

The <scene name='Sandbox_Reserved_197/Cis-proline114/3' target='0'>Asn113-Pro114</scene> peptide bond also resides in a ''cis'' conformation in its folded structure, but exists in the ''trans'' conformation in its unfolded state; therefore, steric restraints imposed by the rest of the protein must be responsible for this ''cis'' conformation. Unlike P93A, the insertion of a <scene name='Sandbox_Reserved_197/P114g/3' target='0'>P114G</scene> point mutation causes the peptide bond to adopt a ''trans'' conformation and causes a 9.3 Å movement of the loop [http://onlinelibrary.wiley.com/doi/10.1110/ps.051610505/full]. The kinetic rate and overall native conformation are not significantly effected by this mutation; however, locally, a rearrangement of the hydrogen-bonding network occurs. Results of this mutation confirm that steric hinderance of the protein can lead to formation of the ''cis'' conformation by a proline and is further energetically stabilized by hydrogen bonding, Van der Waals, and electrostatic interactions within the protein.

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 ==='''Proline Conformation'''===
 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 the ''cis'' conformation than any other amino acid. RNase A contains four proline residues, two reside in the ''cis'' conformation and two in the ''trans'' conformation.<ref name="Lehninger" />  The importance of these conformations are demonstrated based on the structure of RNase A variants with several mutations to the wild type amino acid sequence.
-Located in an outer <scene name='Sandbox_Reserved_197/Tyr92-pro93_loop/3'>loop</scene> of RNase A, the <scene name='Sandbox_Reserved_197/Tyr92-pro93/7' target='0'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. When proline was mutated to alanine, <scene name='Sandbox_Reserved_197/P93a/9' target='0'>P93A</scene>, a ''cis'' conformation still forms at position 93 which is an energetically unfavorable conformation for an alanine residue <ref name ='1'>PMID:9605332</ref>.   Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by other interactions within the folded protein structure. 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, suggesting an important kinetic contribution of ''cis'' prolines to protein folding.<ref name="1" />
+Located in an outer <scene name='Sandbox_Reserved_197/Tyr92-pro93_loop/3'>loop</scene> of RNase A, the <scene name='Sandbox_Reserved_197/Tyr92-pro93/7' target='0'>Tyr92-Pro93</scene> peptide group of RNase A in its native state is found in the ''cis'' conformation. When proline was mutated to alanine, <scene name='Sandbox_Reserved_197/P93a/9' target='0'>P93A</scene>, a ''cis'' conformation still forms at position 93 which is an energetically unfavorable conformation for an alanine residue <ref name ='Tyr92'>PMID:9605332</ref>.   Upon unfolding, Tyr92-Ala93 undergoes isomerization to form its more favorable ''trans'' conformation demonstrating that the ''cis'' conformation is favored by other interactions within the folded protein structure. 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, suggesting an important kinetic contribution of ''cis'' prolines to protein folding.<ref name="Tyr92" />
 The <scene name='Sandbox_Reserved_197/Cis-proline114/3' target='0'>Asn113-Pro114</scene> peptide bond also resides in a ''cis'' conformation in its folded structure, but exists in the ''trans'' conformation in its unfolded state; therefore, steric restraints imposed by the rest of the protein must be responsible for this ''cis'' conformation. Unlike P93A, the insertion of a <scene name='Sandbox_Reserved_197/P114g/3' target='0'>P114G</scene> point mutation causes the peptide bond to adopt a ''trans'' conformation and causes a 9.3 Å movement of the loop [http://onlinelibrary.wiley.com/doi/10.1110/ps.051610505/full]. The kinetic rate and overall native conformation are not significantly effected by this mutation; however, locally, a rearrangement of the hydrogen-bonding network occurs. Results of this mutation confirm that steric hinderance of the protein can lead to formation of the ''cis'' conformation by a proline and is further energetically stabilized by hydrogen bonding, Van der Waals, and electrostatic interactions within the protein.