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Back Types of mechanical clamps

Mechanical clamps in proteins are defined as a structural region which is responsible for the biggest contribution to mechanostability. We determine the mechanical clamps by identifying contacts that break near the largest force peak and then studying dynamical effects associated with a removal of various groups of these contacts. This task is accomplished only for selected proteins.

We divide the mechanical clamps into two main groups: I. involving small strains in localized regions (usually in secondary structures) and II. involving a larger motion of at least one loop made of a segment of the backbone.

Group I: Strain in localized regions

Examples of mechanical clamps belonging to the first group are shown in Figure 1 where the black arrow usually stands for a ¯-strand but sometimes it may have a more generic meaning – it can also indicate a helix. We distinguish the following motifs:

Ia. Elementary motifs
  • S – shearing between parallel β-strands (it may also take place between two helices.
  • SA – shearing between atiparallel β-strands (including the hairpins).
  • Z – unzipping of two β-strands.
  • Za – unzipping of two helices.
  • U – unstructured: shearing between nearby unstructured segments of the backbone.

Ib. Composite motifs
They consist of several elementary motifs

  • SD1 – disconnected: S is followed by S, separated by an essentially strain free region.
  • SD2 – disconnected: SA is followed by SA.
  • SD3 – disconnected: S is followed by SA.
  • SS – supported: the main S motif is flanked by neighboring β-strands which stabilize it. Shearing the main S results also in a shear with the flanking β-strands.
  • T – torsion: multiple S motifs arranged in a bent structure (if the resistance to stretching comes from the links between the S motifs).
  • SB – shear box: a sheared two-strand β-sheet that is placed below a sheared two-helix 'sheet' so that a shear in one strand induces a shear on the helix above.
  • D – a delocalized clamp with multiple elementary clamps exerting comparable resistances to pulling. Some regions can by unstructured.

Group II: Mechanical clamps involving backbone loops

Examples of mechanical clamps belonging to the second group are shown in Figure 2. In most of thesea, the loops arise due to the presence of disulphide bonds, indicated by short solid lines.

  • CK – the cystine knot: shearing takes place inside a cystine knot – a loop that is created by two disulphide bonds.
  • CL1 – the cystine loop: shearing results because one branch of S is pulled by a cystine loop.
  • CL2 – the cystine loop: similar to CL1 but the motion of the cystine loop also drags another piece of the backbone that transmits shear to the other branch of the S motif.
  • CSK – the cystine slipknot motif: involves three disulphide bridges which generate two loops: knot-loop (which is an example of a cystine knot) and a slip-loop. The mechanical resistance to pulling comes from pulling the slip-loop through the knot-loop.
  • SK – the slipknot motif: created by two interacting loops, the slip-loop and the knotloop, that move simulateneously on pulling. If the knot loops shrinks faster than the knot loop then the slipknot gets tightened temporarily and a ”catch bond” is formed. This intermediate and metastable configuration eventually gets untied upon further stretching.

TABLE I: Examples of mechanical clamps - discussed in the literature. The references are provided in the tables summarizing experimental and all-atom data in the BSDB.

1g1cSD2I1(reduced) 1titSI27
1fnhSD210FNIII 1fnhSD212FNIII
1tenSD213FNIII TNFNAll 1nctSI54-I59
1aj3Zα-spectrin 1s35Zβ-spectrin1−4
1cfcZcalmodulin 1qjoZE2lip3
1n11Zankyrin*1 1n11Zankyrin*24
1edhScad1 1edhScad2
1vscScell adhesion VCAM1 1vscSD2cell adhesion VCAM2
1ksrZFLN4 1dqvZC2A
1b6iZaT4 lysozyme 1bnrZbarnase
1j85Smethylotransferase 1ubqSSubiquitin(48-C)
1ubqSSubiquitin(N-C) 1ubqZubiquitin(11-C)
1embSD1GFP(3-212) 1embZGFP(132-212)
1embssGFP(3-132) 1embSD1GFP(117-182)
1pgaSSGB1 1hz6SSprotein L
1anuSD1scaffoldin c2A 1aohSD1scaffoldin c7A
1g1kSD1scaffoldin c1C 1v9eCKBCA II
2o9cSphytochrome 2o9cSphytochrome*

TABLE II: Examples of proteins with small experimental values of Fmax (< 40 pN) as discussed in the literature.

1cyino Fmaxcc6
1bddno Fmax1gb
1rsyno Fmaxc2

TABLE III: Examples of mechanical clamps, as assessed based on our model

PDBmotifs PDBmotifsPDBmotifs PDBmotifs
1bmpCSK 1qtyCSK 2bhkCSK 1lxiCSK
1cz8CSK 2gh0CSK 1wq9CSK 1fltCSK
1fzvCSK 2gyzCSK 1rewCSK 1m4uCSK
1vpfCSK 1c4pSS 1qqrSS 3bmpCSK
1j8sSS 1wq8CSK 1j8rSS 1f3ySS
2vpfCSK 2h64CSK 1kdmCL2 1q56CL2
1rv6CSK 1waqCSK 1reuCSK 1tgjCSK
2pbtSS 2h62CSK 1tgkCSK 2fzlSS
1qu0CL2 1f5fCL2 1dzkCL2 1aohSS
1vscCL2 2c7wCSK 2gyrCSK 1dzjCL2
2sakSS 2bzmCL2 2g7iCL2 1i04CL2
1hqpCL2 1afkCL1 1qozCL1 1lx5CYS
1oxmCL2 1hfhCL1 1aflCL1 1aqpCL1
2g4xCL1 2g4wCL1 2a2gCL2 2bocCL2
1vppCSK 1lm8SA 1ppxSD2 1jrkSD2
1k26SD2 1punSD2 1pusSD2 1oo2SD2
1ssnSD2 1i3vSD2 1pavSB 1qp1D
1amxSA 1ei5SA 1vhpD 1tumD
1f86D 1ui9D 1pqeD 1mg4D

Institute of Physics, Polish Academy of Sciences 2010
Authors: Mateusz Sikora, Marek Cieplak, Joanna I. Sułkowska    Realization: Bartłomiej S. Witkowski