How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

Gunasekaran, Kannan; Nussinov, Ruth

doi:10.1016/j.jmb.2006.09.062

Cited by 122 publications

(113 citation statements)

References 70 publications

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“…Calculations for UmuDЈ 2 based on its NMR structure (14) obtained by using the program MOLMOL (45) show that UmuDЈ 2 has 75 Å of accessible surface area per residue and 22 Å of interface area per residue. These results suggest that the monomeric forms of UmuD and UmuDЈ, if they are ever present in solution, would be disordered and may undergo some disorder-to-order transition upon homodimerization (44). However, recent data show that a disorder-to-order transition is not necessary for homodimerization of one IDP, the T cell receptor -subunit (46).…”

Section: Discussionmentioning

confidence: 94%

“…Structural analysis of a dimeric protein can distinguish between a coupled folding-dimerization event and temporally separated folding and binding steps (44). Calculations for UmuDЈ 2 based on its NMR structure (14) obtained by using the program MOLMOL (45) show that UmuDЈ 2 has 75 Å of accessible surface area per residue and 22 Å of interface area per residue.…”

Section: Discussionmentioning

confidence: 99%

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Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

Simon

Sousa²,

Mohana‐Borges³

et al. 2008

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

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Products of the umuD gene in Escherichia coli play key roles in coordinating the switch from accurate DNA repair to mutagenic translesion DNA synthesis (TLS) during the SOS response to DNA damage. Homodimeric UmuD 2 is up-regulated 10-fold immediately after damage, after which slow autocleavage removes the Nterminal 24 amino acids of each UmuD. The remaining fragment, UmuD 2, is required for mutagenic TLS. The small proteins UmuD2 and UmuD 2 make a large number of specific protein-protein contacts, including three of the five known E. coli DNA polymerases, parts of the replication machinery, and RecA recombinase. We show that, despite forming stable homodimers, UmuD 2 and UmuD 2 have circular dichroism (CD) spectra with almost no ␣-helix or ␤-sheet signal at physiological concentrations in vitro. High protein concentrations, osmolytic crowding agents, and specific interactions with a partner protein can produce CD spectra that resemble the expected ␤-sheet signature. A lack of secondary structure in vitro is characteristic of intrinsically disordered proteins (IDPs), many of which act as regulators. A stable homodimer that lacks significant secondary structure is unusual but not unprecedented. Furthermore, previous single-cysteine cross-linking studies of UmuD 2 and UmuD 2 show that they have a nonrandom structure at physiologically relevant concentrations in vitro. Our results offer insights into structural characteristics of relatively poorly understood IDPs and provide a model for how the umuD gene products can regulate diverse aspects of the bacterial SOS response.natively unfolded ͉ SOS response ͉ unstructured ͉ denatured ͉ DNA repair

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

Simon

Sousa²,

Mohana‐Borges³

et al. 2008

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

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“…These could for instance include analyses of structural deformability, 48,49 sequence conservation, 50,51 or structural features of binding site residues. 52 Finally, another foreseeable extension of the Fleksy approach is the inclusion of crystal waters in the generated structure ensembles. Many cases are known where water molecules play a crucial role in receptor-ligand interactions.…”

Section: Resultsmentioning

confidence: 99%

A Flexible Approach to Induced Fit Docking

2007

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We present Fleksy, a new approach to consider both ligand and receptor flexibility in small molecule docking. Pivotal to our method is the use of a receptor ensemble to describe protein flexibility. To construct these ensembles, we use a backbone-dependent rotamer library and implement the concept of interaction sampling. The latter allows the evaluation of different orientations of ambivalent interaction partners. The docking stage consists of an ensemble-based soft-docking experiment using FlexX-Ensemble, followed by an effective flexible receptor-ligand complex optimization using Yasara. Fleksy produces a set of receptor-ligand complexes ranked using a consensus scoring function combining docking scores and force field energies. Averaged over three cross-docking datasets, containing 35 different receptor-ligand complexes in total, Fleksy reproduces the observed binding mode within 2.0 Å for 78% of the complexes. This compares favorably to the rigid receptor FlexX program, which on average reaches a success rate of 44% for these datasets.

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“…The side chain rotation may be restricted by sequences elsewhere in the receptor, helping to explain the high functional selectivity of these compounds for the M 1 subtype. It is interesting that tryptophan often occurs in protein binding sites that undergo large conformational changes on ligand binding (Gunasekaran and Nussinov, 2007). Tryptophan conformational isomerization may open up novel avenues in drug design.…”

Section: Discussionmentioning

confidence: 99%

Mutagenic Mapping Suggests a Novel Binding Mode for Selective Agonists of M₁ Muscarinic Acetylcholine Receptors

Lebon¹,

Langmead²,

Tehan³

et al. 2008

Mol Pharmacol

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Point mutations and molecular modeling have been used to study the activation of the M 1 muscarinic acetylcholine receptor (mAChR) by the functionally selective agonists 4-n-butyl-1-[4-(2-methylphenyl)-4-oxo-1-butyl]-piperidine (AC-42), and 1-[3-(4-butyl-1-piperidinyl)propyl]-3,4-dihydro-2(1H)-quinolinone (77-LH-28-1), comparing them with N-desmethylclozapine (NDMC) and acetylcholine (ACh). Unlike NDMC and ACh, the activities of AC-42 and 77-LH-28-1 were undiminished by mutations of Tyr404 and Cys407 (transmembrane helix 7), although they were reduced by mutations of Tyr408. Signaling by AC-42, 77-LH-28-1, and NDMC was reduced by L102A and abolished by D105E, suggesting that all three may interact with transmembrane helix 3 at or near the binding site Asp105 to activate the M 1 mAChR. In striking contrast to NDMC and ACh, the affinities of AC-42 and 77-LH-28-1 were increased 100-fold by W101A, and their signaling activities were abolished by Y82A. Tyr82 and Leu102 contact the indole ring of Trp101 in a structural model of the M 1 mAChR. We suggest the hypothesis that the side chain of Trp101 undergoes conformational isomerization, opening a novel binding site for the aromatic side chain of the AC-42 analogs. This may allow the positively charged piperidine nitrogen of the ligands to access the neighboring Asp105 carboxylate to activate signaling following a vector within the binding site that is distinct from that of acetylcholine. NDMC does not seem to use this mechanism. Subtype-specific differences in the free energy of rotation of the side chain and indole ring of Trp101 might underlie the M 1 selectivity of the AC-42 analogs. Tryptophan conformational isomerization may open up new avenues in selective muscarinic receptor drug design.The M 1 muscarinic receptor (mAChR) is an attractive drug target to treat Alzheimer's disease and schizophrenia (Langmead et al., 2008b). The amino acid side chains that contact acetylcholine are modeled on the inward-facing segments of transmembrane (TM) helices 3, 4, 5, 6, and 7 within the outer leaflet of the lipid bilayer (Hulme et al., 2003). Their conservation between the five receptor subtypes has restricted the discovery of selective agonists.AC-42 is a novel ligand that activates M 1 mAChRs selectively (Spalding et al., 2002). Activation is little affected by alanine substitution of the orthosteric binding pocket residues Tyr381 (6.51; Ballesteros and Weinstein, 1995) and Asn382 (6.52) but requires sequences in the N terminus and TM1, extracellular loop 3, and the outer part of TM7. Thus AC-42 may activate M 1 mAChRs from a distinct "ectopic" site (Spalding et al., 2002). Supporting this, AC-42 can display allosteric interactions with N-methyl scopolamine (NMS) and atropine (Langmead et al., 2006). A study of TM3 showed that activation of M 1 mAChRs by AC-42 analogs was unaffected by alanine substitution of Tyr106 (3.33) neighboring the ACh counter-ion Asp105 (3.32) or Ser109 (3.36) one helical turn below but was inhibited by L102A (3.29) and paradoxically very ...

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How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

Cited by 122 publications

References 70 publications

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

A Flexible Approach to Induced Fit Docking

Mutagenic Mapping Suggests a Novel Binding Mode for Selective Agonists of M₁ Muscarinic Acetylcholine Receptors

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How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

Cited by 122 publications

References 70 publications

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

Regulation of Escherichia coli SOS mutagenesis by dimeric intrinsically disordered umuD gene products

A Flexible Approach to Induced Fit Docking

Mutagenic Mapping Suggests a Novel Binding Mode for Selective Agonists of M1 Muscarinic Acetylcholine Receptors

Contact Info

Product

Resources

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Mutagenic Mapping Suggests a Novel Binding Mode for Selective Agonists of M₁ Muscarinic Acetylcholine Receptors