CycloBranch
Branch-cyclic Peptides

Branch-cyclic Peptide Detail Window

The window is opened by a double-click on a row in the output report if a branch-cyclic peptide was identified. The Enter key can also be used if the row is selected.

branchcyclicdetail.png
Direct comparison of experimental spectrum of pyoverdin E with the theoretical spectrum.

See details in Linear Peptide Detail Window, Cyclic Peptide Detail Window and Branched Peptide Detail Window. The differences for branch-cyclic peptides are following:

  • The text window on the right at the bottom (data not shown in the image above) contains a list of all linearized sequences derived from all possible ring opening sites of a branch-cyclic peptide. If the ring is opened, a fragment ion corresponds to a branched peptide. Thus for each linearized sequence (derived from the ring opening), another list of linearized sequences is generated (derived from a branched fragment). The nomenclature of linearized sequences of branch-cyclic peptides simply combines nomenclatures of linearized sequences derived from cyclic and branched peptide sequences. For example, 1-4_5 is a linearized sequence no. 5 of a branched fragment ion arising after a ring opening at the position 1-4.

Toolbar for Branch-cyclic Peptides

See Toolbar for Linear Peptides, Toolbar for Cyclic Peptides and Toolbar for Branched Peptides.


Branch-cyclic Sequence Detection

Series of fragment ions of a branch-cyclic peptide are shown in the following picture.

branchcyclic-series.png
Theoretical fragment ion series generated due to ring opening of a branch-cyclic NRP - (a) a branched fragment, (b) a linear fragment.


A path in the de novo graph corresponding to a branch-cyclic peptide is detected as shown in the following scheme (an edge corresponds to a residue mass of a building block or a sum of residue masses of a combination of building blocks). The options E) and I) are currently not implemented.

branchcyclic-denovo.png
Detection of a path corresponding to a branch-cyclic peptide in a de novo graph.


Since peaks determining the begin and the end of a branch may be missing in an experimental spectrum, the algorithm generates a set of peptide sequence candidates from a path in the graph instead of one sequence candidate. See the following scheme and Branched Sequence Detection for details.

branch-cyclic-detection.png
Peptide sequence candidates generated from a path in a de novo graph (branch-cyclic peptides).



Nomenclature of Branch-cyclic Series

Since branch-cyclic peptides combine properties of cyclic and branched peptides, the nomenclature of branch-cyclic peptides combines nomenclatures of both types of peptides.

Linearized Sequences (Derived from a Ring Opening)

The sequences are derived the same way like linearized sequences of a cyclic peptide with a difference that all building blocks between "(" and ")" are considered as one building block. For example, linearized sequences of pseudacyclin A are generated as follows:

Linearized sequences:
1-5 ~ [Phe]-[Pro]-[Ile]-[Ile] ( [Orn]-[N-Ac-Ile] )
2-1 ~ [Pro]-[Ile]-[Ile] ( [Orn]-[N-Ac-Ile] ) [Phe]
3-2 ~ [Ile]-[Ile] ( [Orn]-[N-Ac-Ile] ) [Phe]-[Pro]
4-3 ~ [Ile] ( [Orn]-[N-Ac-Ile] ) [Phe]-[Pro]-[Ile]
5-4 ~ ( [Orn]-[N-Ac-Ile] ) [Phe]-[Pro]-[Ile]-[Ile]

Reverted linearized sequences:
5-1 ~ ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]-[Pro]-[Phe]
4-5 ~ [Ile]-[Ile]-[Pro]-[Phe] ( [Orn]-[N-Ac-Ile] )
3-4 ~ [Ile]-[Pro]-[Phe] ( [Orn]-[N-Ac-Ile] ) [Ile]
2-3 ~ [Pro]-[Phe] ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]
1-2 ~ [Phe] ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]-[Pro]

pseudacyclin.png
Pseudacyclin A.

Each branch-cyclic peptide may form up to k - 2 branched fragments (or 2*(k - 2) when reverted fragments are considered) where k is the number of monomers forming the ring. Each branch-cyclic peptide may also produce up to 2 linear fragments (or 4 when reverted fragments are considered). These fragments are indicated by the brackets "( ... )" on the left or on the right side of a linearized sequence. Linear fragments of pseudacyclin A are following:

Sequences:
1-5 ~ [Phe]-[Pro]-[Ile]-[Ile] ( [Orn]-[N-Ac-Ile] ) corresponds to a linearized sequence [Phe]-[Pro]-[Ile]-[Ile]-[Orn]-[N-Ac-Ile]
5-4 ~ ( [Orn]-[N-Ac-Ile] ) [Phe]-[Pro]-[Ile]-[Ile] corresponds to a linearized sequence [N-Ac-Ile]-[Orn]-[Phe]-[Pro]-[Ile]-[Ile]

Reverted sequences:
5-1 ~ ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]-[Pro]-[Phe] corresponds to a linearized sequence [N-Ac-Ile]-[Orn]-[Ile]-[Ile]-[Pro]-[Phe]
4-5 ~ [Ile]-[Ile]-[Pro]-[Phe] ( [Orn]-[N-Ac-Ile] ) corresponds to a linearized sequence [Ile]-[Ile]-[Pro]-[Phe]-[Orn]-[N-Ac-Ile]


Linearized Sequences (Derived from a Branched Fragment)

Linearized sequences of a branched fragment are derived similarly to linearized sequences of a branched peptide (see a general fragmentation scheme below). Because of a cyclization in a branch-cyclic peptide, the C-terminal series 1Y and 2Y are replaced with the N-terminal series 3B and 6B.

branchcyclicrotationfragmentation.png
General scheme of linearized sequences and fragmentation of a branched fragment 1-2(3-6)4-5.

Example of Linearized Sequences of a Branched Fragment

Example of linearized sequences of a branched fragment [Pro]-[Ile]-[Ile]([Orn]-[N-Ac-Ile])[Phe] derived from a branch-cyclic peptide pseudacyclin A:

2-1_1 ~ [Pro]-[Ile]-[Ile] ( [Orn]-[N-Ac-Ile] ) [Phe]
2-1_2 ~ [N-Ac-Ile] ( [Orn]-[Ile]-[Ile]-[Pro] ) [Phe]
2-1_3 ~ [Phe] ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]-[Pro]
2-1_4 ~ [Pro]-[Ile]-[Ile] ( [Orn]-[Phe] ) [N-Ac-Ile]
2-1_5 ~ [N-Ac-Ile] ( [Orn]-[Phe] ) [Ile]-[Ile]-[Pro]
2-1_6 ~ [Phe] ( [Orn]-[Ile]-[Ile]-[Pro] ) [N-Ac-Ile]

The same example is shown in the picture below where the fragment ion series are illustrated for each linearized sequence. We assume that a branched fragment is further fragmented only once, thus some b-ions do not exist in the theoretical spectrum (struck out in the following picture).

branchcyclicrotationfragmentation-v2.png
Linearized sequences of a branched fragment of pseudacyclin A (P = proline; I = isoleucine, Or = ornithine; aI = acetylisoleucine; F = phenylalanine).

Example of Linearized Sequences of a Linear Fragment

A linear fragment (e.g., [Phe]-[Pro]-[Ile]-[Ile]([Orn]-[N-Ac-Ile])) may also be obtained instead of a branched one after a ring opening. In this case, the notation of linearized sequences can also be understood as follows:

1-5_1 ~ [Phe]-[Pro]-[Ile]-[Ile] ( [Orn]-[N-Ac-Ile] ) corresponds to [Phe]-[Pro]-[Ile]-[Ile]-[Orn]-[N-Ac-Ile]
1-5_2 ~ [N-Ac-Ile] ( [Orn]-[Ile]-[Ile]-[Pro]-[Phe] ) corresponds to [N-Ac-Ile]-[Orn]-[Ile]-[Ile]-[Pro]-[Phe]
1-5_3 ~ ( [Orn]-[N-Ac-Ile] ) [Ile]-[Ile]-[Pro]-[Phe] corresponds to [N-Ac-Ile]-[Orn]-[Ile]-[Ile]-[Pro]-[Phe]
1-5_4 ~ [Phe]-[Pro]-[Ile]-[Ile] ( [Orn] ) [N-Ac-Ile] corresponds to [Phe]-[Pro]-[Ile]-[Ile]-[Orn]-[N-Ac-Ile]
1-5_5 ~ [N-Ac-Ile] ( [Orn] ) [Ile]-[Ile]-[Pro]-[Phe] corresponds to [N-Ac-Ile]-[Orn]-[Ile]-[Ile]-[Pro]-[Phe]
1-5_6 ~ ( [Orn]-[Ile]-[Ile]-[Pro]-[Phe] ) [N-Ac-Ile] corresponds to [Phe]-[Pro]-[Ile]-[Ile]-[Orn]-[N-Ac-Ile]


Branch-cyclic Siderophores

CycloBranch supports the identification of desferri- and ferri- forms of branch-cyclic siderophores which are nonribosomal peptides. For details, see Linear Nonribosomal Peptide Siderophores.