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secondary structure of protein

by Prof. Marcellus Cormier Published 3 years ago Updated 3 years ago

Secondary structure refers to regular, local structure of the protein backbone, stabilised by intramolecular and sometimes intermolecular hydrogen bonding of amide groups. There are two common types of secondary structure (Figure 11). The most prevalent is the alpha helix
alpha helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O. group of the amino acid located four residues earlier along the protein sequence.
https://en.wikipedia.org › wiki › Alpha_helix
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What is the secondary structure of protein and its types?

Two secondary structure of proteins, the alpha helix, and the beta pleated sheet fulfill these criteria well. Pauling was correct in his prediction. Most defined secondary structures found in proteins are one or the other type. 1. Alpha helix 2. Beta-sheet 3. Fibrous and globular proteins 1. Alpha helix

What does the secondary structure of a protein result from?

The secondary structure of a protein is due to the folding of the polypeptide chain into different folds due to hydrogen bonding and Vander Waal forces. Whereas the tertiary structure of proteins is defined as the arrangement of secondary structure content in 3-dimensional space. While some proteins consist of more than one polypeptide, their ...

How can I predict the protein secondary structure?

To achieve some improvements in the prediction accuracy we could try one of the following:

  • Increase the number of training vectors. Increasing the number of sequences dedicated to training requires a larger curated database of protein structures, with an appropriate distribution of coiled, helical and ...
  • Increase the number of input values. ...
  • Use a different training algorithm. ...
  • Increase the number of hidden neurons. ...

What are the 3 levels of protein structure?

The interactions include:

  • (1) Ionic bonds or salt bridges, ADVERTISEMENTS:
  • (2) Hydrogen bonds,
  • (3) Hydro­phobic bonds, and
  • (4) Disulfide bridges.

What is secondary structure of protein give example?

Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well.

What are the 3 forms in a secondary protein structure?

There are three common secondary structures in proteins, namely alpha helices, beta sheets, and turns. That which cannot be classified as one of the standard three classes is usually grouped into a category called "other" or "random coil".

What is secondary structure example?

A secondary structure of a protein pertains to the folding of a polypeptide chain, resulting in an alpha helix, beta sheet or a random coil structure. Another example of a secondary structure is that of a nucleic acid such as the clover leaf structure of tRNA.

What is primary and secondary structure of protein?

The primary structure is comprised of a linear chain of amino acids. The secondary structure contains regions of amino acid chains that are stabilized by hydrogen bonds from the polypeptide backbone. These hydrogen bonds create alpha-helix and beta-pleated sheets of the secondary structure.

What is an alpha helix and beta sheet?

Alpha-Helix and Beta-Pleated sheets are types of the secondary structure of the protein. They both are shaped by hydrogen bonding between the carbonyl O of one amino acid and the amino H of another.

What are the functions of secondary protein structure?

Secondary structure of the proteins can be used to predict the tertiary structure since predicting only with amino acid sequence may not be sufficient. The secondary structure of proteins is determined by the pattern of hydrogen bonding.

Why is secondary structure important?

The secondary structures play important roles in protein structure and protein folding. We investigate the folding properties of protein by introducing the effect of secondary structure elements. We observed the emergence of several structures with both large average energy gap and high designability.

How are secondary protein structures formed?

The secondary structure arises from the hydrogen bonds formed between atoms of the polypeptide backbone. The hydrogen bonds form between the partially negative oxygen atom and the partially positive nitrogen atom.

What is the difference between secondary and tertiary structures?

A protein's primary structure is defined as the amino acid sequence of its polypeptide chain; secondary structure is the local spatial arrangement of a polypeptide's backbone (main chain) atoms; tertiary structure refers to the three-dimensional structure of an entire polypeptide chain; and quaternary structure is the ...

What is one difference between secondary and tertiary structure in proteins?

The main difference between primary secondary and tertiary structure of protein is that the primary structure of a protein is linear and the secondary structure of a protein can be either an α-helix or β-sheet whereas tertiary structure of a protein is globular.

What are 4 levels of protein structure?

Proteins fold into stable three‐dimensional shapes, or conformations, that are determined by their amino acid sequence. The complete structure of a protein can be described at four different levels of complexity: primary, secondary, tertiary, and quaternary structure.

What is the secondary structure of a protein?

The secondary structure of a protein is due to the folding of the polypeptide chain into different folds due to hydrogen bonding and Vander Waal forces. Whereas the tertiary structure of proteins is defined as the arrangement of secondary structure content in 3-dimensional space. While some proteins consist of more than one polypeptide, ...

What are the three basic levels of structure arrangement of a protein?

There are three basic levels of structure arrangement of a protein which consist of a single polypeptide, called primary protein structure, secondary protein structure, and tertiary protein structure . The primary protein structure is a simple sequence of the amino acids in which they arrange in a polypeptide chain.

How many amino acids are in a helical stretch?

Each turn of the α-helix contains 3.6 amino acids and the helical structure rise along its axis to 5.4 Å. The helical structure in most of the protein consisting of 12 amino acids but in some cases, helical stretch consists of 50 residues.

Why do parallel pleated sheets run in the same direction?

In the parallel β pleated-sheet adjacent polypeptide chains run in the same direction it means that the N- of all the polypeptide chains present at the same direction as their C-terminal present in the same direction. The parallel β pleated-sheet are rarely present as the secondary structure element and they are also less stable than anti-parallel β pleated-sheet because the hydrogen bonds form between adjacent polypeptide chains are longer and their conformation is unfavorable making them weaker.

What is the most common helical structure?

There are different types of helical structure were observed in the proteins but the most common is the α-helix. The helical structure forms due to the presence of the turns in the polypeptide chain and different helical structure are identified on the basis ...

What is the name of the stretch of a polypeptide that joins the strands of a protein

In other cases, polypeptide strands located at different places in a protein can form a hydrogen bond with each other and these are often joined by a long stretch of a polypeptide called loops and sometimes secondary structure like α-helix present in loop regions.

Why is the primary structure important?

The primary structure is very important in defining the structure and function of the protein. Amino acids join each other thorough peptide bonds which are rigid i.e., they do not allow rotation of the two amino acids freely.

What is the secondary structure of proteins?

Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three ...

When was secondary structure first introduced?

The concept of secondary structure was first introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures .

What is SST in biology?

SST is a Bayesian method to assign secondary structure to protein coordinate data using the Shannon information criterion of Minimum Message Length ( MML) inference. SST treats any assignment of secondary structure as a potential hypothesis that attempts to explain ( compress) given protein coordinate data. The core idea is that the best secondary structural assignment is the one that can explain ( compress) the coordinates of a given protein coordinates in the most economical way, thus linking the inference of secondary structure to lossless data compression. SST accurately delineates any protein chain into regions associated with the following assignment types:

Which assignment can explain the coordinates of a given protein coordinates in the most economical way?

The core idea is that the best secondary structural assignment is the one that can explain ( compress) the coordinates of a given protein coordinates in the most economical way, thus linking the inference of secondary structure to lossless data compression.

Which helices have the most hydrogen bonding?

Other helices, such as the 3 10 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix.

Which type of secondary structure is most common in proteins?

The α-helix. The most common type of secondary structure in proteins is the α-helix. Linus Pauling was the first to predict the existence of α-helices. The prediction was confirmed when the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew) was determined by X-ray crystallography.

Why is the loop length shorter in a protein?

Loop length in proteins from organisms living at elevated temperatures (thermophilic organisms) is usually shorter than in protein from lower-temperature family members, presumably to give a protein additional stability at high temperatures, preventing its unfolding and denaturation.

What is the name of the loop between two strands?

When there are only 2 anti-parallel β-strands, like in the figure below, it is called a β-hairpin. The loop between the two strands is called a β-turn. Short turns and longer loops play an important role in protein 3D structures, connecting together strands to strands, strands to α-helices, or helices to helices.

What are structural motifs?

Structural motifs that contain combinations of helices, helices and strands, etc., are closely linked to protein fold. For this reason, when viewing a protein 3D structures, it is an advantage to be able to recognize the secondary structure elements and to identify structural motifs. In the next section we will examine some ...

How many residues are in a helix?

To get a better impression of how a helix looks like, only the main chain of the polypeptide is shown, no side chains. There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6).

Is amino acid sequence conserved?

But in some cases, when a loop has some specific function, for example interaction with another protein, the sequence may be conserved.

What is the helix structure of poly-pro?

chains naturally containing these two amino acids can, therefore, have a left-handed helix structure as collagen.

What are the loops and bends in a protein?

a) Loops and bends (or towers) Around one-third of the amino acids in a protein are part of loops or elbows to U-turns, or beta turns of the peptide chain. Elbows usually bind two antiparallel β strands. They include 2-4 short amino acids. The shorter they are, the fewer possible spatial conformations.

How many amino acids are in a helix?

In general, an α helix consists of 5 to more than 40 amino acids. Amino acids promote the formation of α helix are Ala, Glu, Leu, Met. Amino acids are bad trainers Pro, Gly, Tyr, Ser. Α helices can be hydrophilic, amphipathic or hydrophobic.

What is beta-pleated sheet structure?

The beta-pleated sheet structure can be divided into two types based on the orientation of peptide chains. in a sheet, maybe parallel or antiparallel. In Parallel sheet structure, the orientation of the two polypeptide chains is in the same direction.

Which is more stable, the right or left helix?

The right-handed α helix is more stable than the left-handed helix. This helical shape has no right of 0.54 nm. Certain amino acids (particularly PROLINE) disrupts the α helix. The larger number of acidic (Asp, Glu) or Basic (Lys, Arg and His) amino acids also interfere with α helix structure.

Which amino group is in the opposite direction?

The Amino groups (-NH2) in the two polypeptide chains are in the same direction. Eg: β-Keratin. In Anti-Parallel sheet structure, the orientation of the two polypeptide chains is in the opposite direction. The Amino groups (-NH2) in the two polypeptide chains are in the opposite direction. Eg: Silk Fibroin.

Does rotation occur around peptide bonds?

No rotation occurs around the peptide bond (as it is partly double-bonded in nature). The chain of amino acids forms a rhythmical structure – forming a repeating pattern. That the maximum number of interactions from Hydrogen bonding possible are occurring, independent of the type of residue (amino acid).

What is the secondary structure of proteins?

Secondary Structure. The term secondary structure refers to the interaction of the hydrogen bond donor and acceptor residues of the repeating peptide unit. The two most important secondary structures of proteins, the alpha helix and the beta sheet, were predicted by the American chemist Linus Pauling in the early 1950s.

What are the characteristics of proteins?

The large‐scale characteristics of proteins are consistent with their secondary structures. Proteins can be either fibrous (derived from fibers) or globular (meaning, like a globe). Fibrous proteins are usually important in forming biological structures.

How many residues are in an alpha helix?

In the alpha helix, there is not an integral number of amino acid residues per turn of the helix. There are 3.6 residues per turn in the alpha helix; in other words, the helix will repeat itself every 36 residues, with ten turns of the helix in that interval. Beta sheet.

Which amino group forms rigid peptide bonds that cannot be accommodated in either alpha or beta helices?

This flexibility allows glycine to form turns between secondary structural elements. Conversely, proline , because it contains a secondary amino group, forms rigid peptide bonds that cannot be accommodated in either alpha or beta helices.

Which amino acids are found in alpha helices?

Helix formers include alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, and lysine.

What is the structure of keratin?

The fibrous protein keratin forms structures such as hair and fingernails. The structures of keratin illustrate the importance of secondary structure in giving proteins their overall properties. Alpha keratin is found in sheep wool.

Which amino acid is found in turns?

Serine, glycine, aspartic acid, asparagine, and proline are found most often in turns. No relationship is apparent between the chemical nature of the amino acid side chain and the existence of amino acid in one structure or another.

How many levels of structure are there in proteins?

Many proteins are made up of a single polypeptide chain and have only three levels of structure (the ones we’ve just discussed). However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure.

What are the four levels of protein structure?

To understand how a protein gets its final shape or conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary.

What is the amino acid change in sickle cell anemia?

In sickle cell anemia, one of the polypeptide chains that make up hemoglobin, the protein that carries oxygen in the blood, has a slight sequence change.

How are amino acids connected to each other?

They are connected to one another by disulfide bonds (sulfur-sulfur bonds between cysteines). The A chain also contains an internal disulfide bond. The amino acids that make up each chain of insulin are represented as connected circles, each with the three-letter abbreviation of the amino acid's name.

How many amino acids are in a hemoglobin molecule?

What is most remarkable to consider is that a hemoglobin molecule is made up of two α chains and two β chains, each consisting of about 150 amino acids, for a total of about 600 amino acids in the whole protein.

How many polypeptide chains are there in insulin?

For example, the hormone insulin has two polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown here is cow insulin, although its structure is similar to that of human insulin.) Each chain has its own set of amino acids, assembled in a particular order.

What happens when you change the amino acid sequence of a protein?

Even changing just one amino acid in a protein’s sequence can affect the protein’s overall structure and function . For instance, a single amino acid change is associated with sickle cell anemia, an inherited disease that affects red blood cells.

Chapter: Biochemistry : Structure of Proteins

The polypeptide backbone does not assume a random three-dimensional structure but, instead, generally forms regular arrangements of amino acids that are located near each other in the linear sequence.

A. α-Helix

Several different polypeptide helices are found in nature, but the α-helix is the most common. It is a spiral structure, consisting of a tightly packed, coiled polypeptide backbone core, with the side chains of the component amino acids extending outward from the central axis to avoid interfering sterically with each other (Figure 2.6).

B. β-Sheet

The β-sheet is another form of secondary structure in which all of the peptide bond components are involved in hydrogen bonding (Figure 2.7A). The surfaces of β-sheets appear “pleated,” and these structures are, therefore, often called β-pleated sheets.

C. β-Bends (reverse turns, β-turns)

β-Bends reverse the direction of a polypeptide chain, helping it form a compact, globular shape. They are usually found on the surface of protein molecules and often include charged residues.

D. Nonrepetitive secondary structure

Approximately one half of an average globular protein is organized into repetitive structures, such as the α-helix and β-sheet. The remainder of the polypeptide chain is described as having a loop or coil conformation.

E. Supersecondary structures (motifs)

Globular proteins are constructed by combining secondary structural elements (that is, α-helices, β-sheets, and coils), producing specific geometric patterns or motifs. These form primarily the core (interior) region of the molecule. They are connected by loop regions (for example, β-bends) at the surface of the protein.

Overview

Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.
Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydr…

Types

The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 310 helix and π helix, are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix. Other extended structures such as the polyproline helix and alpha sheet are rare in native state proteins but are often hypothesized as important prot…

Experimental determination

The rough secondary-structure content of a biopolymer (e.g., "this protein is 40% α-helix and 20% β-sheet.") can be estimated spectroscopically. For proteins, a common method is far-ultraviolet (far-UV, 170–250 nm) circular dichroism. A pronounced double minimum at 208 and 222 nm indicate α-helical structure, whereas a single minimum at 204 nm or 217 nm reflects random-coil or β-sheet structure, respectively. A less common method is infrared spectroscopy, which detects dif…

Prediction

Predicting protein tertiary structure from only its amino sequence is a very challenging problem (see protein structure prediction), but using the simpler secondary structure definitions is more tractable.
Early methods of secondary-structure prediction were restricted to predicting the three predominate states: helix, sheet, or random coil. These methods were based on the helix- or she…

Applications

Both protein and nucleic acid secondary structures can be used to aid in multiple sequence alignment. These alignments can be made more accurate by the inclusion of secondary structure information in addition to simple sequence information. This is sometimes less useful in RNA because base pairing is much more highly conserved than sequence. Distant relationships between proteins whose primary structures are unalignable can sometimes be found by second…

See also

• Folding (chemistry)
• Nucleic acid secondary structure
• Translation
• Structural motif
• Protein circular dichroism data bank

Further reading

• Branden C, Author J (1999). Introduction to protein structure (2nd ed.). New York: Garland Science. ISBN 978-0815323051. {{cite book}}: |author= has generic name (help)
• Pauling L, Corey RB (1951). "Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets". Proc. Natl. Acad. Sci. U.S.A. 37 (11): 729–40. Bibcode:1951PNAS...37..729P. doi:10.1073/pnas.37.11.729. PMC 1063460. PMID 16578412. (The original …

External links

• NetSurfP – Secondary Structure and Surface Accessibility predictor
• PROF
• ScrewFit
• PSSpred A multiple neural network training program for protein secondary structure prediction

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      bing_pop_faq_questions
      23
      bing_pop_faq_answers
      24
      bing_tab_faq_questions
      25
      bing_tab_faq_answers
      26
      google_faq_questions
      27
      google_faq_answers
      28
      google_rich_snippet
      29
      google_search_result
      30
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      31
      total_images
      32
      total_videos
      33
      settings
      34
      url_current
      35
      menus
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      sidebar
      37
      i
      38
      __currentLoopData
      39
      loop
      40
      item
    • themes.DevBlog.panels.scripts (resources/views/themes/DevBlog/panels/scripts.blade.php)41blade
      Params
      0
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      1
      app
      2
      errors
      3
      post
      4
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      5
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      6
      updated_at
      7
      bing_rich_snippet_text
      8
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      9
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      bing_news_title
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      bing_news_description
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      bing_videos
      14
      bing_images
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      16
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      17
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      18
      bing_paa_questions
      19
      bing_paa_answers
      20
      bing_slider_faq_questions
      21
      bing_slider_faq_answers
      22
      bing_pop_faq_questions
      23
      bing_pop_faq_answers
      24
      bing_tab_faq_questions
      25
      bing_tab_faq_answers
      26
      google_faq_questions
      27
      google_faq_answers
      28
      google_rich_snippet
      29
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      30
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      31
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      32
      total_videos
      33
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      url_current
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    uri
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    middleware
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    as
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    controller
    App\Http\Controllers\Frontend\json_data\PostController@show
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    where
    file
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    7 statements were executed3.64s
    • select * from `posts` where `published_at` <= '2025-06-25 07:08:54' and `slug` = 'secondary-structure-of-protein' and `posts`.`deleted_at` is null limit 1
      2.12ms/app/Providers/RouteServiceProvider.php:54receivinghelpdeskask
      Metadata
      Bindings
      • 0. 2025-06-25 07:08:54
      • 1. secondary-structure-of-protein
      Backtrace
      • 15. /app/Providers/RouteServiceProvider.php:54
      • 18. /vendor/laravel/framework/src/Illuminate/Routing/Router.php:842
      • 19. Route binding:39
      • 20. /vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php:167
      • 21. /vendor/laravel/framework/src/Illuminate/Foundation/Http/Middleware/VerifyCsrfToken.php:78
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      14.17msmiddleware::checkdate:30receivinghelpdeskask
      Metadata
      Bindings
      • 0. 48234
      • 1. 0
      Backtrace
      • 19. middleware::checkdate:30
      • 20. /vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php:167
      • 21. /vendor/laravel/jetstream/src/Http/Middleware/ShareInertiaData.php:61
      • 22. /vendor/laravel/framework/src/Illuminate/Pipeline/Pipeline.php:167
      • 23. /vendor/laravel/framework/src/Illuminate/Routing/Middleware/SubstituteBindings.php:50
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      2.31ms/vendor/outl1ne/nova-menu-builder/src/helpers.php:32receivinghelpdeskask
      Metadata
      Bindings
      • 0. header
      Backtrace
      • 15. /vendor/outl1ne/nova-menu-builder/src/helpers.php:32
      • 17. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 18. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 19. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
      • 20. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:205
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      610μs/vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35receivinghelpdeskask
      Metadata
      Bindings
      • 0. 1
      Backtrace
      • 19. /vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35
      • 20. /vendor/outl1ne/nova-menu-builder/src/helpers.php:33
      • 22. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 23. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 24. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
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      580μs/vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35receivinghelpdeskask
      Metadata
      Backtrace
      • 24. /vendor/outl1ne/nova-menu-builder/src/Models/Menu.php:35
      • 25. /vendor/outl1ne/nova-menu-builder/src/helpers.php:33
      • 27. /vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 28. /vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:45
      • 29. /vendor/laravel/framework/src/Illuminate/Routing/Route.php:261
    • select `id`, `post_title`, `slug` from `posts` where `status` = 'publish' and `posts`.`deleted_at` is null order by RAND() limit 10
      3.62s/app/View/Composers/SidebarView.php:22receivinghelpdeskask
      Metadata
      Bindings
      • 0. publish
      Backtrace
      • 14. /app/View/Composers/SidebarView.php:22
      • 15. /app/View/Composers/SidebarView.php:12
      • 16. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:124
      • 17. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:162
      • 20. /vendor/laravel/framework/src/Illuminate/View/Concerns/ManagesEvents.php:177
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      870μsview::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15receivinghelpdeskask
      Metadata
      Bindings
      • 0. 39403
      Backtrace
      • 21. view::2dd102cf0462e89a4d4d8bc77355d767652bf9aa:15
      • 23. /vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:108
      • 24. /vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 25. /vendor/livewire/livewire/src/ComponentConcerns/RendersLivewireComponents.php:69
      • 26. /vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:61
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    1
    Outl1ne\MenuBuilder\Models\MenuItem
    1
    Outl1ne\MenuBuilder\Models\Menu
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    App\Models\JsonPostContent
    1
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