Proteopedia - User contributions [en]

User talk:Vini Maheshwar

2026-03-11T13:24:50Z

Vini Maheshwar:

'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! . [[User:Eric Martz|Eric Martz]] 21:06, 18 November 2025 (UTC)

Hello,
I created this account for a university assignment and would like to request that my account be deleted or disabled.
Username: Vini Maheshwar
Thank you.

File:Figure 2a Overall fold and disulfide architecture of CART(48–89).png

2026-03-11T13:21:45Z

Vini Maheshwar:

{{delete}}

Overall fold and disulfide architecture of CART(48–89)

File:Figure 2a Overall fold and disulfide architecture of CART(48–89).png

2026-03-11T13:19:11Z

Vini Maheshwar:

{{delete|Author request — uploaded by mistake}}

Overall fold and disulfide architecture of CART(48–89)

File:1HY9 hydrophobic patch (1).png

2026-03-11T13:18:09Z

Vini Maheshwar: Requesting deletion – created for an assignment

{{delete|Created for a course assignment}}

1HY9 hydrophobic patch - Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

File:1HY9 hydrophobic patch (2).png

2026-03-11T13:17:25Z

Vini Maheshwar: Requesting deletion – created for an assignment

{{delete|Created for a course assignment}}

Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

File:Disulfide architecture of CART(48–89).png

2026-03-11T13:14:24Z

Vini Maheshwar: Requesting deletion – created for an assignment

File:1HY9 positively charged cluster.png

2026-03-11T13:13:13Z

Vini Maheshwar: Requesting deletion – created for an assignment

{{delete|Created for a course assignment}}

1HY9 positively charged cluster - A cluster of basic residues forms a prominent charged surface. This positively charged region is strikingly surface-exposed and may interact with negatively charged receptor surfaces, enhance solubility, and help the peptide associate with membranes.

Cart

2026-03-11T13:11:46Z

Vini Maheshwar: Requesting deletion – assignment page

{{delete|Created for a course assignment}}

==Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide==
<StructureSection load='1hy9' size='340' side='right' caption='Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide' scene='1hy9'>
'''CART''' (Cocaine- and Amphetamine-Regulated Transcript) is a neuropeptide found primarily in the hypothalamus of the brain, where it plays an important role in regulating appetite and energy balance. CART expression increases after cocaine or amphetamine exposure, but it is now best known as an '''anorectic (appetite-suppressing) peptide''' regulated by the hormone leptin. Injections of CART into the brain reduce normal feeding, starvation-induced feeding, and block the strong feeding response caused by neuropeptide Y (NPY).
The biologically active region of CART is a small, disulfide-rich C-terminal fragment (residues 48–89), whose three-dimensional structure reveals a compact scaffold stabilized by '''three disulfide bonds'''.

----

== Biological Background ==
CART is synthesized as a larger precursor peptide that undergoes multiple processing steps. In humans, cleavage at a Lys-Arg site produces two major fragments:

'''CART(1–39)''' — N-terminal fragment

'''CART(42–89)''' — C-terminal fragment

The C-terminal fragment contains six cysteine residues that form three disulfide bonds. This C-terminal piece is highly conserved across species and is the '''minimal biologically active form''' capable of suppressing feeding in rodents, fish, and other animals.

Although the '''biologically active C-terminal peptide''' is '''CART(42–89)''', residues '''42–47 do not form any stable structure'''. In the NMR experiments, these residues were completely disordered and produced no interpretable distance restraints. The first residue that participates in the folded, disulfide-stabilized core is residue 48. Therefore the '''structurally well-defined region is CART(48–89)'''.

CART is produced in hypothalamic nuclei that regulate appetite. Its levels rise in response to leptin, the hormone produced by adipose tissue that signals sufficient energy stores. CART belongs to a growing family of neuropeptides that modulate hunger, satiety, and energy expenditure.

----

== Structural Description ==

=== Overall fold ===
The structure of CART(48–89) reveals a compact mini-protein dominated by loops and turns, held together by a tight network of three disulfide bonds. This architecture results in an unusually stable fold for such a short peptide.

The three disulfide bonds (connecting half-cystines at positions 55–61, 73–75, and 81–88) create a rigid scaffold similar to a '''cystine-knot'''. This fold allows the peptide to maintain a stable three-dimensional shape even in harsh environments.

=== Secondary structure elements ===
Although small, CART contains identifiable structural motifs:

A '''short antiparallel β-sheet''' between residues 62–64 and 69–71

A '''second tiny β-sheet''' between residues 81–82 and 87–88

'''Three turns''': Type I turn (residues 56–59); Type II′ turn (residues 65–68); Type II turn (residues 76–79)

These structural features combine with the disulfide network to produce a compact, globular fold.

=== Core packing ===
The peptide’s interior is tightly packed around the disulfide bridges. '''Ala62''' lies at the center of this core, surrounded by hydrophobic side chains. All six cysteine residues are buried, consistent with the need to protect the disulfide knot.

----

== Functional Surface Features ==
Although the core is rigid, the surface contains distinct regions that likely contribute to biological function.

=== 1. Positively charged patch ===

[[Image:1HY9_positively_charged_cluster.png]]

A cluster of basic residues forms a prominent charged surface:

'''Arg64'''

'''Lys65'''

'''Arg68'''

'''Lys71'''

This positively charged region is strikingly surface-exposed and may interact with negatively charged receptor surfaces, enhance solubility, and help the peptide associate with membranes.

NMR data reveal that Lys71 is unusually well restrained, suggesting it forms a structurally anchored point within this charged pocket..

=== 2. Hydrophobic hotspot ===

[[Image:1HY9_hydrophobic_patch_(1).png]]
[[Image:1HY9_hydrophobic_patch_(2).png]]

On the opposite face of the molecule lies a contiguous hydrophobic surface composed of:

'''Phe84'''

'''Leu85'''

'''Leu86'''

'''Leu89'''

Hydrophobic patches such as this are common recognition elements in '''peptide–protein interactions''' and represent a plausible '''primary receptor-binding interface'''.
Its high degree of conservation strengthens the hypothesis that this region plays a key functional role.

The presence of two contrasting surface features—a charged patch and a hydrophobic hotspot—suggests that CART likely engages its receptor through a '''bipartite binding interface''' involving both electrostatic and hydrophobic contacts.

----

== Structure–Function Insights ==

=== Only the C-terminal fragment is active ===
NMR measurements showed that residues 48–89 fold into a compact, ordered structure, whereas the N-terminal half of the precursor (including residues 42–47) is disordered and produces no long-range NOEs, indicating a lack of structure. This explains why:

CART(1–39) and other N-terminal fragments have no satiety function.

CART(42–89) and CART(48–89) are the only physiologically active forms.

Biological data confirm that only fragments containing the triple-disulfide core show anorectic activity after intracerebroventricular injection.

=== Stability from disulfide bonds ===

[[Image:Disulfide_architecture_of_CART(48–89).png]]

CART contains '''six''' cysteine residues ('''Cys55, Cys61, Cys73, Cys75, Cys81, Cys88'''), paired in the unusual pattern:

'''I–III''' (Cys55–Cys73)

'''II–V''' (Cys61–Cys81)

'''IV–VI''' (Cys75–Cys88)

This I–III, II–V, IV–VI pattern is different from classical knottins, but still produces a homologous cystine knot fold. The disulfide pattern locks the peptide into one dominant conformation, shields the hydrophobic core, allows the peptide to be resistant to denaturation and proteolysis, and maintains a consistent receptor-binding surface.

=== Loops determine specificity ===
Although the core is highly rigid, the surrounding loops differ in length and shape compared to classical knottins:

'''Loop 64–69''' is the '''largest''' among the seven related peptides in the structural comparison.

'''Loop 84–86''' is the '''shortest''' among the aligned knottin structures.

These loops show fewer NOEs and higher dihedral-angle variability, are partially flexible, and likely encode functional specificity because the rigid core provides shape, but the loops determine exact receptor interactions.

Thus, CART preserves a '''knottin-like fold''' but modifies loop architecture to achieve its own biological function.

=== Distinct surface patches suggest possible receptor-binding interfaces ===
The solved structure reveals two major surface features:

A. A large positively charged cluster

Formed by Arg64, Lys65, Arg68, and importantly Lys71, which is structurally restrained (has extensive NOEs, indicating a fixed position rather than a floppy side chain).

This charged patch may interact with negatively charged surfaces on a receptor, help orient the peptide relative to the membrane, or contribute to solubility and targeting.

Lys71 specifically forms a positive “pocket” that may represent a binding hotspot.

B. A hydrophobic hotspot

A continuous hydrophobic surface is formed by Phe84, Leu85, Leu86, Leu89 (and smaller hydrophobic neighbors like Pro53, Val52, Val63, Leu72).

This hydrophobic patch is large and contiguous, remains solvent-exposed despite being hydrophobic, and is a strong candidate for the primary receptor-binding interface.

Therefore, area is a possible hot spot for receptor interaction due to its size and conservation.

=== Structural features correlate with biological activity ===
Fragments shorter than CART(48–89)—such as CART(49–63) in goldfish—show reduced anorectic activity (page 6) because they contain parts of the β-hairpin (residues 62–64, 69–71), but lack the full disulfide knot and hydrophobic patch.

This supports the idea that the full cystine knot is required for stable receptor binding, while the hydrophobic and charged surfaces are key functional epitopes.

Thus, the structure directly explains why only certain cleavage products have physiological potency.

</StructureSection>

----

== References ==
1. Ludvigsen S., Thim L., Blom A.M., Wulff B.S. (2001). Solution Structure of the Satiety Factor CART Reveals New Functionality of a Well-Known Fold. Biochemistry 40:9082–9088.
PDB ID: 1HY9

2. Hydrophobic surface coloring and molecular visualization were generated using the Mol* Viewer (Sehnal et al., 2021).
Sehnal D., Bittrich S., Deshpande M., et al. (2021).
Mol* Viewer: modern web-based molecular graphics for large complexes.
''Nucleic Acids Research'', 49(W1): W431–W437.
Available at: https://molstar.org

3. Electrostatic surface potential was calculated using the APBS software package (Jurrus et al., 2018) via the APBS web server.
Jurrus E., Engel D., Star K., et al. (2018).
Improving the APBS biomolecular solvation software suite.
''Protein Science'', 27(1): 112–128.
Available at: https://apbs.biochem.missouri.edu/

APBS Electrostatics Web Server
https://apbs.bioexcel.eu

== Note ==
This page was created as part of the '''BI3323-Aug2025 assignment'''.
[[Category:BI3323-Aug2025]]

Cart

2025-11-30T12:39:16Z

Vini Maheshwar: New page: ==Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide== <StructureSection load='1hy9' size='340' side='right' caption='Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide...

==Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide==
<StructureSection load='1hy9' size='340' side='right' caption='Cocaine- and Amphetamine-Regulated Transcript (CART) Peptide' scene='1hy9'>
'''CART''' (Cocaine- and Amphetamine-Regulated Transcript) is a neuropeptide found primarily in the hypothalamus of the brain, where it plays an important role in regulating appetite and energy balance. CART expression increases after cocaine or amphetamine exposure, but it is now best known as an '''anorectic (appetite-suppressing) peptide''' regulated by the hormone leptin. Injections of CART into the brain reduce normal feeding, starvation-induced feeding, and block the strong feeding response caused by neuropeptide Y (NPY).
The biologically active region of CART is a small, disulfide-rich C-terminal fragment (residues 48–89), whose three-dimensional structure reveals a compact scaffold stabilized by '''three disulfide bonds'''.

----

== Biological Background ==
CART is synthesized as a larger precursor peptide that undergoes multiple processing steps. In humans, cleavage at a Lys-Arg site produces two major fragments:

'''CART(1–39)''' — N-terminal fragment

'''CART(42–89)''' — C-terminal fragment

The C-terminal fragment contains six cysteine residues that form three disulfide bonds. This C-terminal piece is highly conserved across species and is the '''minimal biologically active form''' capable of suppressing feeding in rodents, fish, and other animals.

Although the '''biologically active C-terminal peptide''' is '''CART(42–89)''', residues '''42–47 do not form any stable structure'''. In the NMR experiments, these residues were completely disordered and produced no interpretable distance restraints. The first residue that participates in the folded, disulfide-stabilized core is residue 48. Therefore the '''structurally well-defined region is CART(48–89)'''.

CART is produced in hypothalamic nuclei that regulate appetite. Its levels rise in response to leptin, the hormone produced by adipose tissue that signals sufficient energy stores. CART belongs to a growing family of neuropeptides that modulate hunger, satiety, and energy expenditure.

----

== Structural Description ==

=== Overall fold ===
The structure of CART(48–89) reveals a compact mini-protein dominated by loops and turns, held together by a tight network of three disulfide bonds. This architecture results in an unusually stable fold for such a short peptide.

The three disulfide bonds (connecting half-cystines at positions 55–61, 73–75, and 81–88) create a rigid scaffold similar to a '''cystine-knot'''. This fold allows the peptide to maintain a stable three-dimensional shape even in harsh environments.

=== Secondary structure elements ===
Although small, CART contains identifiable structural motifs:

A '''short antiparallel β-sheet''' between residues 62–64 and 69–71

A '''second tiny β-sheet''' between residues 81–82 and 87–88

'''Three turns''': Type I turn (residues 56–59); Type II′ turn (residues 65–68); Type II turn (residues 76–79)

These structural features combine with the disulfide network to produce a compact, globular fold.

=== Core packing ===
The peptide’s interior is tightly packed around the disulfide bridges. '''Ala62''' lies at the center of this core, surrounded by hydrophobic side chains. All six cysteine residues are buried, consistent with the need to protect the disulfide knot.

----

== Functional Surface Features ==
Although the core is rigid, the surface contains distinct regions that likely contribute to biological function.

=== 1. Positively charged patch ===

[[Image:1HY9_positively_charged_cluster.png]]

A cluster of basic residues forms a prominent charged surface:

'''Arg64'''

'''Lys65'''

'''Arg68'''

'''Lys71'''

This positively charged region is strikingly surface-exposed and may interact with negatively charged receptor surfaces, enhance solubility, and help the peptide associate with membranes.

NMR data reveal that Lys71 is unusually well restrained, suggesting it forms a structurally anchored point within this charged pocket..

=== 2. Hydrophobic hotspot ===

[[Image:1HY9_hydrophobic_patch_(1).png]]
[[Image:1HY9_hydrophobic_patch_(2).png]]

On the opposite face of the molecule lies a contiguous hydrophobic surface composed of:

'''Phe84'''

'''Leu85'''

'''Leu86'''

'''Leu89'''

Hydrophobic patches such as this are common recognition elements in '''peptide–protein interactions''' and represent a plausible '''primary receptor-binding interface'''.
Its high degree of conservation strengthens the hypothesis that this region plays a key functional role.

The presence of two contrasting surface features—a charged patch and a hydrophobic hotspot—suggests that CART likely engages its receptor through a '''bipartite binding interface''' involving both electrostatic and hydrophobic contacts.

----

== Structure–Function Insights ==

=== Only the C-terminal fragment is active ===
NMR measurements showed that residues 48–89 fold into a compact, ordered structure, whereas the N-terminal half of the precursor (including residues 42–47) is disordered and produces no long-range NOEs, indicating a lack of structure. This explains why:

CART(1–39) and other N-terminal fragments have no satiety function.

CART(42–89) and CART(48–89) are the only physiologically active forms.

Biological data confirm that only fragments containing the triple-disulfide core show anorectic activity after intracerebroventricular injection.

=== Stability from disulfide bonds ===

[[Image:Disulfide_architecture_of_CART(48–89).png]]

CART contains '''six''' cysteine residues ('''Cys55, Cys61, Cys73, Cys75, Cys81, Cys88'''), paired in the unusual pattern:

'''I–III''' (Cys55–Cys73)

'''II–V''' (Cys61–Cys81)

'''IV–VI''' (Cys75–Cys88)

This I–III, II–V, IV–VI pattern is different from classical knottins, but still produces a homologous cystine knot fold. The disulfide pattern locks the peptide into one dominant conformation, shields the hydrophobic core, allows the peptide to be resistant to denaturation and proteolysis, and maintains a consistent receptor-binding surface.

=== Loops determine specificity ===
Although the core is highly rigid, the surrounding loops differ in length and shape compared to classical knottins:

'''Loop 64–69''' is the '''largest''' among the seven related peptides in the structural comparison.

'''Loop 84–86''' is the '''shortest''' among the aligned knottin structures.

These loops show fewer NOEs and higher dihedral-angle variability, are partially flexible, and likely encode functional specificity because the rigid core provides shape, but the loops determine exact receptor interactions.

Thus, CART preserves a '''knottin-like fold''' but modifies loop architecture to achieve its own biological function.

=== Distinct surface patches suggest possible receptor-binding interfaces ===
The solved structure reveals two major surface features:

A. A large positively charged cluster

Formed by Arg64, Lys65, Arg68, and importantly Lys71, which is structurally restrained (has extensive NOEs, indicating a fixed position rather than a floppy side chain).

This charged patch may interact with negatively charged surfaces on a receptor, help orient the peptide relative to the membrane, or contribute to solubility and targeting.

Lys71 specifically forms a positive “pocket” that may represent a binding hotspot.

B. A hydrophobic hotspot

A continuous hydrophobic surface is formed by Phe84, Leu85, Leu86, Leu89 (and smaller hydrophobic neighbors like Pro53, Val52, Val63, Leu72).

This hydrophobic patch is large and contiguous, remains solvent-exposed despite being hydrophobic, and is a strong candidate for the primary receptor-binding interface.

Therefore, area is a possible hot spot for receptor interaction due to its size and conservation.

=== Structural features correlate with biological activity ===
Fragments shorter than CART(48–89)—such as CART(49–63) in goldfish—show reduced anorectic activity (page 6) because they contain parts of the β-hairpin (residues 62–64, 69–71), but lack the full disulfide knot and hydrophobic patch.

This supports the idea that the full cystine knot is required for stable receptor binding, while the hydrophobic and charged surfaces are key functional epitopes.

Thus, the structure directly explains why only certain cleavage products have physiological potency.

</StructureSection>

----

== References ==
1. Ludvigsen S., Thim L., Blom A.M., Wulff B.S. (2001). Solution Structure of the Satiety Factor CART Reveals New Functionality of a Well-Known Fold. Biochemistry 40:9082–9088.
PDB ID: 1HY9

2. Hydrophobic surface coloring and molecular visualization were generated using the Mol* Viewer (Sehnal et al., 2021).
Sehnal D., Bittrich S., Deshpande M., et al. (2021).
Mol* Viewer: modern web-based molecular graphics for large complexes.
''Nucleic Acids Research'', 49(W1): W431–W437.
Available at: https://molstar.org

3. Electrostatic surface potential was calculated using the APBS software package (Jurrus et al., 2018) via the APBS web server.
Jurrus E., Engel D., Star K., et al. (2018).
Improving the APBS biomolecular solvation software suite.
''Protein Science'', 27(1): 112–128.
Available at: https://apbs.biochem.missouri.edu/

APBS Electrostatics Web Server
https://apbs.bioexcel.eu

== Note ==
This page was created as part of the '''BI3323-Aug2025 assignment'''.
[[Category:BI3323-Aug2025]]

File:1HY9 positively charged cluster.png

2025-11-30T12:13:47Z

Vini Maheshwar: uploaded a new version of "Image:1HY9 positively charged cluster.png"

1HY9 positively charged cluster - A cluster of basic residues forms a prominent charged surface. This positively charged region is strikingly surface-exposed and may interact with negatively charged receptor surfaces, enhance solubility, and help the peptide associate with membranes.

File:1HY9 positively charged cluster.png

2025-11-30T12:07:51Z

Vini Maheshwar: uploaded a new version of "Image:1HY9 positively charged cluster.png"

File:Disulfide architecture of CART(48–89).png

2025-11-30T12:06:01Z

Vini Maheshwar: uploaded a new version of "Image:Disulfide architecture of CART(48–89).png": Reverted to version as of 11:37, 30 November 2025

File:Disulfide architecture of CART(48–89).png

2025-11-30T12:05:42Z

Vini Maheshwar: uploaded a new version of "Image:Disulfide architecture of CART(48–89).png"

File:1HY9 hydrophobic patch (2).png

2025-11-30T11:51:59Z

Vini Maheshwar: Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

File:1HY9 hydrophobic patch (1).png

2025-11-30T11:50:51Z

Vini Maheshwar: 1HY9 hydrophobic patch - Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

1HY9 hydrophobic patch - Hydrophobic patches such as this are common recognition elements in peptide–protein interactions and represent a plausible primary receptor-binding interface.

File:1HY9 positively charged cluster.png

2025-11-30T11:47:00Z

Vini Maheshwar: 1HY9 positively charged cluster - A cluster of basic residues forms a prominent charged surface. This positively charged region is strikingly surface-exposed and may interact with negatively charged receptor surfaces, enhance solubility, and help the pept

File:Disulfide architecture of CART(48–89).png

2025-11-30T11:37:42Z

Vini Maheshwar: uploaded a new version of "Image:Disulfide architecture of CART(48–89).png": Disulfide architecture of CART(48–89)

File:Disulfide architecture of CART(48–89).png

2025-11-30T11:34:28Z

Vini Maheshwar:

File:Figure 2a Overall fold and disulfide architecture of CART(48–89).png

2025-11-30T07:09:51Z

Vini Maheshwar:

Overall fold and disulfide architecture of CART(48–89)
{{delete|Author request — uploaded by mistake}}

File:Figure 2a Overall fold and disulfide architecture of CART(48–89).png

2025-11-30T07:00:42Z

Vini Maheshwar: Overall fold and disulfide architecture of CART(48–89)

Overall fold and disulfide architecture of CART(48–89)