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PubMed2000

The conserved motif in hydrophilic loop 2/3 and loop 8/9 of the lactose permease of Escherichia coli. Analysis of suppressor mutations.

The major facilitator superfamily (MFS) of transport proteins, which includes the lactose permease of Escherichia coli, contains a conserved motif G-X-X-X-D/E-R/K-X-G-R/K-R/K in the loops that connect transmembrane segments 2 and 3, and transmembrane segments 8 and 9. In three previous studies (Jessen-Marshall, A.E., & Brooker, R.J. 1996. J. Biol. Chem. 271:1400-1404; Jessen-Marshall, A.E., Parker, N., & Brooker, R.J. 1997. J. Bacteriol. 179:2616-2622; and Pazdernik, N., Cain, S.M., & Brooker, R.J. 1997. J. Biol. Chem. 272:26110-26116), suppressor mutations at twenty different sites were identified which restore function to mutant permeases that have deleterious mutations in the conserved loop 2/3 or loop 8/9 motif. In the current study, several of these second-site suppressor mutations have been separated from the original mutation in the conserved motif. The loop 2/3 suppressors were then coupled to a loop 8/9 mutation (P280L) and the loop 8/9 suppressors were coupled to a loop 2/3 mutation (i.e., G64S) to determine if the suppressors could restore function only to a loop 2/3 mutation, a loop 8/9 mutation, or both. The single parent mutations changing the first position in loop 2/3 (i.e., G64S) and loop 8/9 (i.e., P280L) had less than 4% lactose transport activity. Interestingly, most of the suppressors were very inhibitory when separated from the parent mutation. Two suppressors, A50T and G370V, restored substantial transport activity when individually coupled to the mutation in loop 2/3 and also when coupled to the corresponding mutation in loop 8/9. In other words, these suppressors could alleviate a defect imposed by mutations in either half of the permease. From a kinetic analysis, these suppressors were shown to exert their effects by increasing the V(max) values for lactose transport compared with the single G64S and P280L strains. These results are discussed within the context of our model in which the two halves of the lactose permease interact at a rotationally symmetrical interface, and that lactose transport is mediated by conformational changes at the interface.

Amino Acid Motifs↗

PubMed1997

Porins of Haemophilus influenzae type b mutated in loop 3 and in loop 4.

Porin (341 amino acids; mass of 37,782 Da) in the outer membrane of Haemophilus influenzae type b (Hib) permits diffusion into the periplasm of small solutes up to a molecular mass of 1400 Da. Molecular modeling of Hib porin identified its structural similarities to OmpF of Escherichia coli and disclosed for Hib porin a shorter length of loop 3 and a longer length of loop 4. By site-directed mutagenesis of the porin gene ompP2, mutant porins were constructed to contain 6 or 12 amino acid deletions either in loop 3 or in surface-exposed loop 4. Wild type Hib porin and mutant porins were expressed in a nontypeable H. influenzae strain deleted for the ompP2 gene. The mutant porins were purified and reconstituted into planar bilayers, tested for channel formation and compared with wild type Hib porin. Mutant Haemophilus porin possessing a 6-amino acid deletion in loop 3 displayed a broad distribution of single channel conductance values, while deletion of 12 amino acids from the same loop destabilized the porin channel. By comparison, deletion of 6 or of 12 amino acids from loop 4 of Hib porin resulted in an increased single channel conductance (1.15 and 1.05 nanosiemens, respectively) compared with wild type Hib porin (0. 85 nanosiemens). The C3 epitope of the poliovirus VP1 capsid protein was inserted either into loop 3 or into loop 4 of Hib porin. By flow cytometry, the C3 epitope was detected as surface-exposed in strains expressing C3 insertion in loop 4; in strains expressing C3 insertion in loop 3, the epitope was inaccessible. We propose that loop 4 of Hib porin, although surface-accessible, is oriented toward the central axis of the pore and that deletions in this loop increase the single channel conductance by widening the pore entrance.

Amino Acid Sequence↗

PubMed1998

The third intracellular loop of the rat gonadotropin-releasing hormone receptor couples the receptor to Gs- and G(q/11)-mediated signal transduction pathways: evidence from loop fragment transfection in GGH3 cells.

The GnRH receptor (GnRH-R) belongs to the rhodopsin/beta-adrenergic family of G protein-coupled receptors. The intracellular domains of these receptors, particularly the regions closest to the plasma membrane in intracellular loops 2 (2i) and 3 (3i) as well as some regions located in the membrane-proximal end of the COOH-terminus, are frequently important sites for G protein coupling and specificity determination. Although studies in mouse and human GnRH-R have identified loop 2i as a critical determinant for coupling the receptor to the G(q/11)-mediated signal transduction pathway, given the functional similarity among the members of this particular G protein-coupled receptor subfamily and the fact that the GnRH-R lacks the typical intracellular COOH-terminal domain of its superfamily (a potential site for G protein coupling), we investigated the possibility that loop 3i of this receptor also participates in GnRH-R coupling to G proteins. GGH(3)1' cells, a pituitary-derived cell line that expresses a functional rat GnRH-R coupled to both Gs and G(q/11) proteins, were transiently transfected with a plasmid DNA containing a complementary DNA (cDNA) coding for the entire loop 3i of the GnRH-R as well as with other expression plasmids containing cDNAs encoding loop 3i of other Gs-, G(i/o)-, or G(q/11)-coupled receptors. The effects of coexpression of these loops with the wild-type GnRH-R on inositol phosphate (IP) production, cAMP accumulation, and PRL release were then examined. Transfection of GGH(3)1' cells with the cDNA for loop 3i of the rat GnRH-R (efficiency, 35-45%) maximally inhibited buserelin-stimulated IP turnover by 20% as well as cAMP accumulation and PRL secretion by 30%. This attenuation in cellular responses to a GnRH agonist was statistically significant (P < 0.05) compared with the responses exhibited by GGH(3)1' cells transfected with a control plasmid and stimulated with the same GnRH agonist. Transfection of minigenes coding for loop 3i of the M1Ach-muscarinic and the alpha1B-adrenergic (G(q/11)-coupled) receptors resulted in 25-55% inhibition of maximal GnRH-evoked IP turnover. Paradoxically, loop 3i from the M1Ach-muscarinic receptor also maximally inhibited GnRH agonist-stimulated cAMP accumulation and PRL release by 40% (both effects mediated through activation of the Gs protein). Transfection of loop 3i from the D1A -dopamine receptor (coupled to the Gs protein) produced a selective attenuation (40%) in Gs-mediated cellular responses. In contrast, receptor/G protein coupling appeared unaffected by expression of loop 3i domains derived from two receptors coupled to G(i/o) proteins (M2Ach-muscarinic and alpha2A-adrenergic receptors). These data indicate that the third intracellular loop of the rat GnRH-R is involved in receptor G(q/11) protein coupling and/or selectivity, and in the GGH(3)1' cell line, this loop is also involved in signal transduction mediated through the Gs protein pathway.

Amino Acid Sequence↗

PubMed1999

Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries.

Lac repressor (LacI) forms DNA loops which are critical for efficient operator binding and transcriptional repression. Designed DNA loops formed on three constructs with lac operators bracketing phased A-tract bends were characterized by mobility shift, footprinting, and DNA cyclization and topology. Operator dyad axes point either in or out relative to the sequence-induced curvature. Possible conformations suggested from X-ray structures of LacI and LacI.DNA include "wrapping away" (WA), "simple loop" (SL), and "wrapping toward" (WT) models. The WA loop should be preferentially stabilized by the outward operators, the SL and WT loops by the inward operators. Competition experiments demonstrated increased loop stability for all the bent constructs, with the SL/WT construct supporting hyperstable loops (t1/2 of days). This offers a general approach to stabilizing multi-protein DNA complexes on short DNA. DNA cyclization of loops gave minicircle products with altered topologies. WA constructs afforded relaxed and positive topoisomers, and cyclization kinetics indicated slow interconversion of precursors to the two topoisomers. The SL/WT construct gave a relaxed topoisomer, with a small amount of negative supercoil. These results suggest that while it is possible to force the WA loop to form (as in a model proposed from the LacI.DNA structure), the most stable loop geometry is different, probably a U-shape around an extended LacI tetramer. The topological results show how a protein-induced positive supercoil can be reconciled with LacI's preference for binding negatively supercoiled DNA. We suggest that looping proteins can affect the assembly of subsequent proteins by controlling loop topology.

Bacterial Proteins↗

PubMed2001

A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple.

The architecture of G-G-G-G tetrad-aligned DNA quadruplexes in monovalent cation solution is dependent on the directionality of the four strands, which in turn are defined by loop connectivities and the guanine syn/anti distribution along individual strands and within individual G-G-G-G tetrads. The smallest unimolecular G-quadruplex belongs to the d(G2NnG2NnG2NnG2) family, which has the potential to form two stacked G-tetrads linked by Nn loop connectivities. Previous studies have focused on the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2), where Nn was T2 for the first and third connecting loops and TGT for the middle connecting loop. This DNA aptamer in K(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(anti)-G(syn)-G(anti) tetrads, adjacent strands which are antiparallel to each other and edge-wise connecting T2, TGT and T2 loops. We now report on the NMR-based solution structure of the d(G2T4G2CAG2GT4G2T) sequence, which differs from the thrombin-binding DNA aptamer sequence in having longer first (T4) and third (GT4) loops and a shorter (CA) middle loop. This d(G2T4G2CAG2GT4G2T) sequence in Na(+) cation solution forms a unimolecular G-quadruplex stabilized by two stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads, adjacent strands which have one parallel and one antiparallel neighbors and distinct non-edge-wise loop connectivities. Specifically, the longer first (T4) and third (GT4) loops are of the diagonal type while the shorter middle loop is of the double chain reversal type. In addition, the pair of stacked G-G-G-G tetrads are flanked on one side by a G-(T-T) triad and on the other side by a T-T-T triple. The distinct differences in strand directionalities, loop connectivities and syn/anti distribution within G-G-G-G tetrads between the thrombin-binding DNA aptamer d(G2T2G2TGTG2T2G2) quadruplex reported previously, and the d(G2T4G2CAG2GT4G2T) quadruplex reported here, reinforces the polymorphic nature of higher-order DNA architectures. Further, these two small unimolecular G-quadruplexes, which are distinct from each other and from parallel-stranded G-quadruplexes, provide novel targets for ligand recognition. Our results demonstrate that the double chain reversal loop connectivity identified previously by our laboratory within the Tetrahymena telomere d(T2G4)4 quadruplex, is a robust folding topology, since it has now also been observed within the d(G2T4G2CAG2GT4G2T) quadruplex. The identification of a G-(T-T) triad and a T-T-T triple, expands on the available recognition alignments for base triads and triples.

Aptamers, Nucleotide↗

PubMed2001

Loop ileostomy versus loop colostomy for defunctioning low anastomoses during rectal cancer surgery.

Several studies have compared loop ileostomy with loop colostomy to defunction colorectal anastomoses. The discordant results may be due to the heterogeneity of the indications. We therefore performed a retrospective study to compare the two procedures in a homogeneous group of patients operated on electively for rectal cancer. Among 462 consecutive patients undergoing rectal resection for cancer during 1986-1998, 60 had a loop colostomy and 107 a loop ileostomy to defunction a low anastomosis. The two groups were similar with respect to age, gender, obesity, tumor stage, and duration before closure (109 vs. 104 days; p = 0.28). All the stoma-related complications that occurred after construction and after closure of the stoma were recorded. There were no stoma-related deaths in the two groups. After stoma construction, the morbidity rate was significantly higher following loop colostomy than after loop ileostomy (35% vs. 19%; p = 0.02). After stoma closure the complication rate was significantly higher in the colostomy group than in the ileostomy group (34% vs. 12%; p = 0.004). The risk of surgical reintervention related to the morbidity of both construction and closure of the stoma was twice as high after loop colostomy than after loop ileostomy (22% vs. 9%; p = 0.03). The results of this study showed that, in our experience, the overall stoma-related morbidity and risk of reoperation were significantly lower after loop ileostomy than after loop colostomy. This suggests that loop ileostomy is the best procedure for defunctioning colorectal anastomoses electively. We therefore recommend using a loop ileostomy during rectal cancer surgery.

Adult↗

PubMed2000

Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site.

Loop-loop interactions among nucleic acids constitute an important form of molecular recognition in a variety of biological systems. In HIV-1, genomic dimerization involves an intermolecular RNA loop-loop interaction at the dimerization initiation site (DIS), a hairpin located in the 5' noncoding region that contains an autocomplementary sequence in the loop. Only two major DIS loop sequence variants are observed among natural viral isolates. To investigate sequence and structural constraints on genomic RNA dimerization as well as loop-loop interactions in general, we randomized several or all of the nucleotides in the DIS loop and selected in vitro for dimerization-competent sequences. Surprisingly, increasing interloop complementarity above a threshold of 6 bp did not enhance dimerization, although the combinations of nucleotides forming the theoretically most stable hexanucleotide duplexes were selected. Noncanonical interactions contributed significantly to the stability and/or specificity of the dimeric complexes as demonstrated by the overwhelming bias for noncanonical base pairs closing the loop and covariations between flanking and central loop nucleotides. Degeneration of the entire loop yielded a complex population of dimerization-competent sequences whose consensus sequence resembles that of wild-type HIV-1. We conclude from these findings that the DIS has evolved to satisfy simultaneous constraints for optimal dimerization affinity and the capacity for homodimerization. Furthermore, the most constrained features of the DIS identified by our experiments could be the basis for the rational design of DIS-targeted antiviral compounds.

Codon, Initiator↗

PubMed2003

The new loop-loop interactions between the peripheral domains and three-dimensional model of Tetrahymena group I intron.

The long-range interactions between the peripheral domains of Tetrahymena group I intron were studied by NMR. The 20mer RNA contained the 9.1a loop region (AUGCAA) and the 17mer RNA contained the 2.1 loop region (AGAUUGC) were synthesized and studied by NMR. They form both hairpin structures at low NaCl concentration. The 20mer RNA forms dimer by loop-loop interaction, while the 17mer RNA is monomer. On the addition of the 17mer to the 20mer, the new imino proton signals induced by the interaction between the 9.1a and 2.1 loops were not observed. It is found that the 9.1a loop-loop interaction (GCAA-GCAA) with two base pairs prefers to that between the 9.1a and 2.1 loops (GCAA-UUGC) with four base pairs. By my model of intact folding structure containing A-minor tertiary interaction and the compared with sequence, it is presumed that the 9.1a loop does not bind to the 2.1 loop, but to the 5c loop (UGCAA), while the 2.1 loop binds to 3' exon (UAA).

Animals↗

PubMed1995

Identifying the mechanism of protein loop closure: a molecular dynamics simulation of the Bacillus stearothermophilus LDH loop in solution.

The 'loop' involving residues 98-110 in Bacillus stearothermophilus lactate dehydrogenase (BSLDH) is of great interest as substrate-induced 'loop' closure is thought to be rate-limiting and essential in catalyzing the reaction and in determining substrate specificity. Consequently, we have explored the mechanism underlying 'loop' opening in BSLDH through a molecular dynamics simulation at high temperature (1000 K) in the presence of explicit solvent, starting from the X-ray structure of BSLDH complexed with the co-enzyme NAD+ and oxamate at 2.5 A. During the simulation, a significant conformational change occurred, as evidenced by sharp dihedral angle transitions, hydrogen bond breaking and formation and large root mean square deviations from the starting structure; these changes define the criteria for 'loop' opening. The mechanical elements responsible for 'loop' opening, i.e. 'loop' hinges and flap, are defined through a combination of order parameters, dihedral angle changes and their correlations and the dynamical cross-correlation map of atomic displacements for the 'loop' residues. The results indicate that the 'loop' consists of two flexible hinge regions on either side of a relatively rigid three-residue segment that undergoes a significant spatial displacement during 'loop' opening. 'Loop' opening is made possible through an array of correlated dihedral angle changes and intra-'loop' rearrangements of hydrogen-bond interactions. The present findings are compared to previous work related to 'loop' opening and site-directed mutagenesis experiments.

Amino Acid Sequence↗

PubMed1995

Determinants of RNA hairpin loop-loop complex stability.

Complexes formed by RNA hairpin loops with complementary loop sequences derived from Escherichia coli RNA I and RNA II, which are involved in the control of DNA replication of plasmid ColE1, have been analyzed to determine the sequence and structural elements required to achieve full affinity. Of particular interest is the origin of the enhanced stability of the complex formed by hairpin loops whose loop sequences have been inverted 5' to 3' with respect to wild-type sequences. Full complementarity of the two interacting loops is required to achieve full or enhanced affinity, while the stems of the two hairpins can differ. The major determinant of enhanced affinity lies in the base-pairs formed at positions 1 and 7 of the loops, together with the two base-pairs of each stem which are closest to the loop. Sequence variation in the middle of the loops, or further down the stem away from the loops, exerts only a modest influence on complex stability. We incorporate these results into a model for the loop-loop interaction which accounts for the importance of positions one and seven and the first two nucleotides of the stem, while providing potentially unique structures for recognition by the RNA one modulator protein.

Base Sequence↗

PubMed2004

Dynamic elastic pressure-volume loops in healthy pigs recorded with inspiratory and expiratory sinusoidal flow modulation. Relationship to static pressure-volume loops.

OBJECTIVE: The objective was to analyse relationships between inspiratory and expiratory static and dynamic elastic pressure-volume (P(el)/V) curves in healthy pigs. DESIGN: The modulated low flow method was developed to allow studies also of the expiratory P(el)/V curves. Static P(el)/V (P(el,st)/V) and dynamic P(el)/V (P(el,dyn)/V) loops were studied in healthy pigs. SETTING: Animal research laboratory in a university hospital. MATERIAL: Ten healthy anaesthetised and paralysed pigs. INTERVENTIONS AND MEASUREMENTS: A computer controlled a Servo Ventilator 900C with respect to respiratory rate, inspiratory flow and expiratory pressure to achieve a sinusoidal modulation of inspiration and expiration for determination of P(el,dyn)/V loops from zero end-expiratory pressure (ZEEP) and from a positive end-expiratory pressure (PEEP) of 6 cmH(2)O to 20, 35 and 50 cmH(2)O. The same system was used for studies of P(el,st)/V loops with the flow-interruption method from ZEEP and PEEP to 35 cmH(2)O. Recordings were analysed with an iterative technique. RESULTS: The feasibility of automated determination of P(el,dyn)/V loops was demonstrated. Differences between P(el,dyn)/V and P(el,st)/V loops were explained by viscoelastic behaviour. P(el,st)/V loops recorded from PEEP to 35 cmH(2)O showed no significant hysteresis, indicating a non-significant surface tension hysteresis. P(el,dyn)/V loops from PEEP and both P(el,st)/V and P(el,dyn)/V loops from ZEEP to 35 cmH(2)O showed hysteresis. This indicates that lung collapse/re-expansion caused P(el)/V loop hysteresis which, in P(el,dyn)/V loops, was augmented by viscoelastic behaviour. CONCLUSIONS: Viscoelasticity influences P(el,dyn)/V curves. Hysteresis caused by surface tension merits re-evaluation. Lung collapse and re-expansion may be indicated by hysteresis of P(el)/V loops.

Analysis of Variance↗

PubMed2003

Triggering loops and enzyme function: identification of loops that trigger and modulate movements.

Enzyme function often involves a conformational change. There is a general agreement that loops play a vital role in correctly positioning the catalytically important residues. Nevertheless, predicting the functional loops and most importantly their role in enzyme function remains a difficult task. A major reason for this difficulty is that loops that undergo conformational change are frequently not well conserved in their primary sequence. beta1,4-Galactosyltransferase is one such enzyme. There, the amino acid sequence of a long loop that undergoes a large conformational change upon substrate binding is not well conserved. Our molecular dynamics simulations show that the large conformational change in the long loop is brought about by a second, interacting loop. Interestingly, while the structural change of the second loop is much smaller than that of the long loop, its sequence (particularly glycine residues) is highly conserved. We further examine the generality of the proposition that there are loops that trigger movements but nevertheless show little or no structural changes in crystals. We focus on two other enzymes, enolase and lipase. We chose these enzymes, since they too undergo conformational change upon ligand binding, however, they have different folds and different functions. Through multiple sets of simulations we show that the conformational change of the functional loop(s) is brought about through communication of flexibility by triggering loops that have several glycine residues. We further propose that similar to the conservation of common favorable fold types and structural motifs, evolution has also conserved common "skillful" mechanisms. Mechanisms may be conserved across different folds, sequences and functions, with adaptation to specific enzymatic roles.

Apoenzymes↗

PubMed1994

Stabilities of nucleotide loops bridging the pyrimidine strands in DNA pyrimidine.purine.pyrimidine triplexes: special stability of the CTTTG loop.

Recent studies of DNA hairpin loops have shown considerable dependence of the stability on the sequence of the loop [Senior, M., Jones, R. A., & Breslauer, K. J. (1988a) Proc. Natl. Acad. Sci. U.S.A. 85, 6242-6246; Xodo, L. E., Manzini, G., Quadrifoglio, F., van der Marel, G., & van Boom, J. H. (1989) Biochimie 71, 793-803; Hirao, I., Nishimura, Y., Tagawa, Y., Watanabe, K., & Miura, K. (1992) Nucleic Acids Res. 20, 3891-3896]. Analogous studies have not, until now, been carried out with loops in triple helices. We report the results from experiments in which we examine the relative stabilities of pentanucleotide loops that bridge between the pyrimidine strands in DNA pyr.pur.pyr triple helices. There are two types of loops that are defined by the relative orientation of the purine strand: a 5'-loop and a 3'-loop. The sequences examined in this study are the bimolecular triplexes formed between 5'-dTTCTTTTCL1TTTL5CTTTTCTT (loop nucleotides are underlined, and L1 and L5 represent varied nucleotides) and the two purine strands, 5'-dAAGAAAAG-3' and 5'-dGAAAAGAA-3'. The first and last nucleotides in the loop are varied, since stacking interactions may be strongest at these positions [Senior et al., 1988a; Senior, M., Jones, R. A., & Breslauer, K. J. (1988b) Biochemistry 27, 3879-3885], and we examine 14 sequence combinations for each loop type. Thermal denaturation studies carried out at pH 7.0 indicate considerable variation in the stabilities of these loops.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1999

A novel loop-loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex.

The yeast Saccharomyces cerevisiae ribosomal protein L30 negatively autoregulates its production by binding to a helix-loop-helix structure formed in its pre-mRNA and its mRNA. A three-dimensional solution structure of the L30 protein in complex with its regulatory RNA has been solved using NMR spectroscopy. In the complex, the helix-loop-helix RNA adopts a sharply bent conformation at the internal loop region. Unusual RNA features include a purine stack, a reverse Hoogsteen base pair (G11anti-G56syn) and highly distorted backbones. The L30 protein is folded in a three-layer alpha/beta/alpha sandwich topology, and three loops at one end of the sandwich make base-specific contacts with the RNA internal loop. The protein-RNA binding interface is divided into two clusters, including hydrophobic and aromatic stacking interactions centering around G56, and base-specific hydrogen-bonding contacts to A57, G58 and G10-U60 wobble base pair. Both the protein and the RNA exhibit a partially induced fit for binding, where loops in the protein and the internal loop in the RNA become more ordered upon complex formation. The specific interactions formed between loops on L30 and the internal loop on the mRNA constitute a novel loop-loop recognition motif where an intimate RNA-protein interface is formed between regions on both molecules that lack regular secondary structure.

Allosteric Regulation↗

PubMed2001

The second cytoplasmic loop of metabotropic glutamate receptor functions at the third loop position of rhodopsin.

G protein-coupled receptors identified so far are classified into at least three major families based on their amino acid sequences. For the family of receptors homologous to rhodopsin (family 1), the G protein activation mechanism has been investigated in detail, but much less for the receptors of other families. To functionally compare the G protein activation mechanism between rhodopsin and metabotropic glutamate receptor (mGluR), which belong to distinct families, we prepared a set of bovine rhodopsin mutants whose second or third cytoplasmic loop was replaced with either the second or third loop of Gi/Go- or Gq-coupled mGluR (mGluR6 or mGluR1). Among these mutants, the mutants in which the second or third loop was replaced with the corresponding loop of mGluR exhibited no G protein activation ability. In contrast, the mutant whose third loop was replaced with the second loop of Gi/Go-coupled mGluR6 efficiently activated Gi but not Gt: this activation profile is almost identical with those of the mutant rhodopsins whose third loop was replaced with those of the Gi/Go-coupled receptors in family 1 [Yamashita et al. (2000) J. Biol. Chem. 275, 34272-34279]. The mutant whose third loop was replaced with the second loop of Gq-coupled mGluR1 partially retained the Gi coupling ability of rhodopsin, which is in contrast to the fact that all the rhodopsin mutants having the third loops of Gq-coupled receptors in family 1 exhibit no detectable Gi activation. These results strongly suggest that the molecular architectures of rhodopsin and mGluR are different, although the G protein activation mechanism involving the cytoplasmic loops is common.

Amino Acid Sequence↗

PubMed2002

The dual role of a loop with low loop contact distance in folding and domain swapping.

Alpha helices, beta strands, and loops are the basic building blocks of protein structure. The folding kinetics of alpha helices and beta strands have been investigated extensively. However, little is known about the formation of loops. Experimental studies show that for some proteins, the formation of a single loop is the rate-determining step for folding, whereas for others, a loop (or turn) can misfold to serve as the hinge loop region for domain-swapped species. Computer simulations of an all-atom model of fragment B of Staphylococcal protein A found that the formation of a single loop initiates the dominant folding pathway. On the other hand, the stability analysis of intermediates suggests that the same loop is a likely candidate to serve as a hinge loop for domain swapping. To interpret the simulation result, we developed a simple structural parameter: the loop contact distance (LCD), or the sequence distance of contacting residues between a loop and the rest of the protein. The parameter is applied to a number of other proteins, including SH3 domains and prion protein. The results suggest that a locally interacting loop (low LCD) can either promote folding or serve as the hinge region for domain swapping. Thus, there is an intimate connection between folding and domain swapping, a possible cause of misfolding and aggregation.

Computer Simulation↗

PubMed2005

Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops.

In protein structure prediction, a central problem is defining the structure of a loop connecting 2 secondary structures. This problem frequently occurs in homology modeling, fold recognition, and in several strategies in ab initio structure prediction. In our previous work, we developed a classification database of structural motifs, ArchDB. The database contains 12,665 clustered loops in 451 structural classes with information about phi-psi angles in the loops and 1492 structural subclasses with the relative locations of the bracing secondary structures. Here we evaluate the extent to which sequence information in the loop database can be used to predict loop structure. Two sequence profiles were used, a HMM profile and a PSSM derived from PSI-BLAST. A jack-knife test was made removing homologous loops using SCOP superfamily definition and predicting afterwards against recalculated profiles that only take into account the sequence information. Two scenarios were considered: (1) prediction of structural class with application in comparative modeling and (2) prediction of structural subclass with application in fold recognition and ab initio. For the first scenario, structural class prediction was made directly over loops with X-ray secondary structure assignment, and if we consider the top 20 classes out of 451 possible classes, the best accuracy of prediction is 78.5%. In the second scenario, structural subclass prediction was made over loops using PSI-PRED (Jones, J Mol Biol 1999;292:195-202) secondary structure prediction to define loop boundaries, and if we take into account the top 20 subclasses out of 1492, the best accuracy is 46.7%. Accuracy of loop prediction was also evaluated by means of RMSD calculations.

Models, Molecular↗

PubMed1999

A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops.

BACKGROUND: Camelid serum contains a large fraction of functional heavy-chain antibodies - homodimers of heavy chains without light chains. The variable domains of these heavy-chain antibodies (VHH) have a long complementarity determining region 3 (CDR3) loop that compensates for the absence of the antigen-binding loops of the variable light chains (VL). In the case of the VHH fragment cAb-Lys3, part of the 24 amino acid long CDR3 loop protrudes from the antigen-binding surface and inserts into the active-site cleft of its antigen, rendering cAb-Lys3 a competitive enzyme inhibitor. RESULTS: A dromedary VHH with specificity for bovine RNase A, cAb-RN05, has a short CDR3 loop of 12 amino acids and is not a competitive enzyme inhibitor. The structure of the cAb-RN05-RNase A complex has been solved at 2.8 A. The VHH scaffold architecture is close to that of a human VH (variable heavy chain). The structure of the antigen-binding hypervariable 1 loop (H1) of both cAb-RN05 and cAb-Lys3 differ from the known canonical structures; in addition these H1 loops resemble each other. The CDR3 provides an antigen-binding surface and shields the face of the domain that interacts with VL in conventional antibodies. CONCLUSIONS: VHHs adopt the common immunoglobulin fold of variable domains, but the antigen-binding loops deviate from the predicted canonical structure. We define a new canonical structure for the H1 loop of immunoglobulins, with cAb-RN05 and cAb-Lys3 as reference structures. This new loop structure might also occur in human or mouse VH domains. Surprisingly, only two loops are involved in antigen recognition; the CDR2 does not participate. Nevertheless, the antigen binding occurs with nanomolar affinities because of a preferential usage of mainchain atoms for antigen interaction.

Amino Acid Sequence↗