SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

Hildebrand, Peter W.; Goede, Andrean; Bauer, Raphael André; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preißner, Robert

doi:10.1093/nar/gkp338

Cited by 89 publications

(78 citation statements)

References 23 publications

(33 reference statements)

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“…Only the highly flexible (25, 26) loop C2 of R* needs to be rearranged to avoid a clash with G t . We applied a search routine to compute low energy C2 loop conformations taken from known protein structures (see SI Appendix) (53). The best scored loop structure displays a conformation between the C2 structures of rhodopsin or opsin (4, 27, 28) on the one side and the ␤ 1 -and ␤ 2 -adrenergic receptors (29)(30)(31) or the A 2A -adenosine receptor (32) on the other side (Fig.…”

Section: Discussionmentioning

confidence: 99%

Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface

Scheerer¹,

Heck²,

Goede

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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Extracellular signals prompt G protein-coupled receptors (GPCRs) to adopt an active conformation (R*) and catalyze GDP/GTP exchange in the ␣-subunit of intracellular G proteins (G␣␤␥). Kinetic analysis of transducin (Gt␣␤␥) activation shows that an intermediary R*⅐Gt␣␤␥⅐GDP complex is formed that precedes GDP release and formation of the nucleotide-free R*⅐G protein complex. Based on this reaction sequence, we explore the dynamic interface between the proteins during formation of these complexes. We start from the R* conformation stabilized by a G t␣ C-terminal peptide (G␣CT) obtained from crystal structures of the GPCR opsin. Molecular modeling allows reconstruction of the fully elongated C-terminal ␣-helix of Gt␣ (␣5) and shows how ␣5 can be docked to the open binding site of R*. Two modes of interaction are found. One of them -termed stable or S-interaction -matches the position of the G␣CT peptide in the crystal structure and reproduces the hydrogen-bonding networks between the C-terminal reverse turn of G␣CT and conserved E(D)RY and NPxxY(x)5,6F regions of the GPCR. The alternative fit -termed intermediary or I-interaction -is distinguished by a tilt (42°) and rotation (90°) of ␣5 relative to the S-interaction and shows different ␣5 contacts with the NPxxY(x)5,6F region and the second cytoplasmic loop of R*. From the 2 ␣5 interactions, we derive a ''helix switch'' mechanism for the transition of R*⅐Gt␣␤␥⅐GDP to the nucleotide-free R*⅐G protein complex that illustrates how ␣5 might act as a transmission rod to propagate the conformational change from the receptor-G protein interface to the nucleotide binding site.G protein coupled receptors (GPCRs) use the free energy of agonist binding to transmit physical or chemical signals into the cell. Bound agonists stabilize the 7 transmembrane (7TM) helix bundle of the receptor in an active conformation (R*). R* in turn interacts with intracellular heterotrimeric G proteins (G␣␤␥, G) to catalyze the exchange of GDP for GTP in the G␣ subunit and thus activate downstream effectors. According to classical receptor theory, R* is also stabilized by G protein binding (1). We used a synthetic peptide derived from the C terminus of the ␣-subunit of transducin (G␣CT), the key binding site for the receptor (2, 3), to stabilize and crystallize the R* conformation of opsin (4, 5). Opsin is the ligand-free form of the photoreceptor rhodopsin, and transducin (G t ␣␤␥, G t ) is its cognate G protein. X-ray structure analysis of the R*⅐G␣CT complex revealed that the cytoplasmic side of the TM5/TM6 helix pair (corresponding to the cytoplasmic loop C3 of the 7TM bundle) forms a mitt-like structure in which G␣CT is held. The contacts with R* induce in G␣CT an ␣-helical conformation with a C-terminal reverse turn (C-cap) (4, 6, 7), which is recognized by the receptor on the basis of its geometry (4).In GPCR mediated signal transduction, the signal is eventually established in the GTP-bound form of the G protein, which is the form that activates downstream effectors. The key step in whi...

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Section: Discussionmentioning

confidence: 99%

Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface

Scheerer¹,

Heck²,

Goede

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

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“…Missing loops (residues 1-18, 130-140, 465-482, 586-593, 657-659, 685-691 and 720-735) were added using SuperLooper (Hildebrand et al, 2009) which models loops based on templates from protein structures to fill in gaps in the protein structure. The two Ca 2+ ions bound to the two subunits were preserved for the simulation of the Ca 2+ -activated system, and removed for the simulation of the Ca 2+ -free system.…”

Section: Preparation Of Membrane-embedded Scramblasementioning

confidence: 99%

Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase

Jiang

Hartzell

et al. 2018

Biophysical Journal

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From bacteria to mammals, different phospholipid species are segregated between the inner and outer leaflets of the plasma membrane by ATP-dependent lipid transporters. Disruption of this asymmetry by ATP-independent phospholipid scrambling is important in cellular signaling, but its mechanism remains incompletely understood. Using MD simulations coupled with experimental assays, we show that the surface hydrophilic transmembrane cavity exposed to the lipid bilayer on the fungal scramblase nhTMEM16 serves as the pathway for both lipid translocation and ion conduction across the membrane. Ca 2+ binding stimulates its open conformation by altering the structure of transmembrane helices that line the cavity. We have identified key amino acids necessary for phospholipid scrambling and validated the idea that ions permeate TMEM16 Cl -channels via a structurally homologous pathway by showing that mutation of two residues in the pore region of the TMEM16A Ca 2+ -activated Cl -channel convert it into a robust scramblase.

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“…Modeling, energy optimization and assignment of the secondary structures were performed with the Swiss-PdbViewer software (Guex and Peitsch 1997). Missing loops were modeled using the tool SuperLooper (Hildebrand et al 2009). It was not possible to model the region 305-329 of N.sua.BSMT2, because the insertion of about 20 amino acids is too long to obtain a reasonable structure prediction.…”

Section: Determination Of Gene Expression Patterns By Rt-pcrmentioning

confidence: 99%

Enzymatic, expression and structural divergences among carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana

Hippauf

Michalsky²,

Huang

et al. 2009

Plant Mol Biol

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Methyl salicylate and methyl benzoate have important roles in a variety of processes including pollinator attraction and plant defence. These compounds are synthesized by salicylic acid, benzoic acid and benzoic acid/salicylic acid carboxyl methyltransferases (SAMT, BAMT and BSMT) which are members of the SABATH gene family. Both SAMT and BSMT were isolated from Nicotiana suaveolens, Nicotiana alata, and Nicotiana sylvestris allowing us to discern levels of enzyme divergence resulting from gene duplication in addition to species divergence. Phylogenetic analyses showed that Nicotiana SAMTs and BSMTs evolved in separate clades and the latter can be differentiated into the BSMT1 and the newly established BSMT2 branch. Although SAMT and BSMT orthologs showed minimal change coincident with species divergences, substantial evolutionary change of enzyme activity and expression patterns occurred following gene duplication. After duplication, the BSMT enzymes evolved higher preference for benzoic acid (BA) than salicylic acid (SA) whereas SAMTs maintained ancestral enzymatic preference for SA over BA. Expression patterns are largely complementary in that BSMT transcripts primarily accumulate in flowers, leaves and stems whereas SAMT is expressed mostly in roots. A novel enzyme, nicotinic acid carboxyl methyltransferase (NAMT), which displays a high degree of activity with nicotinic acid was discovered to have evolved in N. gossei from an ancestral BSMT. Furthermore a SAM-dependent synthesis of methyl anthranilate via BSMT2 is reported and contrasts with alternative biosynthetic routes previously proposed. While BSMT in flowers is clearly involved in methyl benzoate synthesis to attract pollinators, its function in other organs and tissues remains obscure.

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SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

Cited by 89 publications

References 23 publications

Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface

Structural and kinetic modeling of an activating helix switch in the rhodopsin-transducin interface

Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase

Enzymatic, expression and structural divergences among carboxyl O-methyltransferases after gene duplication and speciation in Nicotiana

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