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PubMed2000

Amino acid repeat patterns in protein sequences: their diversity and structural-functional implications.

All the protein sequences from SWISS-PROT database were analyzed for occurrence of single amino acid repeats, tandem oligo-peptide repeats, and periodically conserved amino acids. Single amino acid repeats of glutamine, serine, glutamic acid, glycine, and alanine seem to be tolerated to a considerable extent in many proteins. Tandem oligo-peptide repeats of different types with varying levels of conservation were detected in several proteins and found to be conspicuous, particularly in structural and cell surface proteins. It appears that repeated sequence patterns may be a mechanism that provides regular arrays of spatial and functional groups, useful for structural packing or for one to one interactions with target molecules. To facilitate further explorations, a database of Tandem Repeats in Protein Sequences (TRIPS) has been developed and is available at URL: http://www.ncl-india.org/trips.

Amino Acid Sequence↗

PubMedDate not supplied

[Structure-activity analysis of ribonuclease A and related proteins].

A detailed analysis of noncovalent interactions in the RNase A molecule was carried out. For this purpose, contact maps based on structural data were constructed. Three hydrophobic nuclei and five microclusters were identified, and their quantitative parameters were calculated. The contacts between amino acid residues of the active center and the hydrophobic nuclei were established. The distribution of the charged amino acid residues on the of RNase A surface was shown. The data obtained was discussed in the context of the ribonuclease A family. The substitutions seen from the alignment of amino acid sequences in the family might have influence on the spatial structure of different parts of RNase A and their mutual orientation and, consequently on the biological activity of family members.

Amino Acid Sequence↗

PubMed1998

Studies of conformational isomerism in alpha-melanocyte stimulating hormone by design of cyclic analogues.

Results of energy calculations for alpha-MSH (alpha-melanocyte stimulating hormone, Ac-Ser1-Tyr2-Ser3-Met4-Glu5-His6-Phe7-Arg8-Trp9- Gly10-Lys11-Pro12-Val13-NH2) and [D-Phe7] alpha-MSH were used for design of cyclic peptides with the general aim to stabilize different conformational isomers of the parent compound. The minimal structural modifications of the conformationally flexible Gly10 residue, as substitutions for L-Ala, D-Ala, or Aib (replacing of hydrogen atoms by methyl groups), were applied to obtain octa- and heptapeptide analogues of alpha-MSH(4-11) and alpha-MSH(5-11), which were cyclized by lactam bridges between the side chains in positions 5 and 11. Some of these analogues, namely those with substitutions of the Gly10 residue with L-Ala or Aib, showed biological activity potencies on frog skin comparable to the potency of the parent tridecapeptide hormone. Additional energy calculations for designed cyclic analogues were used for further refinement of the model for the biologically active conformations of the His-Phe-Arg-Trp "message" sequence within the sequences of alpha-MSH and [D-Phe7]alpha-MSH. In such conformations the aromatic moieties of the side chains of the His6, L/D-Phe7, and Trp9 residues form a continuous hydrophobic "surface," presumably interacting with a complementary receptor site. This feature is characteristic for low-energy conformers of active cyclic analogues, but it is absent in the case of inactive analogues. This particular spatial arrangement of functional groups involved in the message sequence is very close for alpha-MSH and [D-Phe7]alpha-MSH, as well as for biologically active cyclic analogues despite differences of dihedral angle values for corresponding low-energy conformations.

Amino Acid Sequence↗

PubMed2001

Involvement of the dorsal anterior cingulate cortex in temporal behavioral sequencing: subregional analysis of the medial prefrontal cortex in rat.

We recently demonstrated that rats with dorsal anterior cingulate (ACd) cortical lesions were disrupted in the acquisition of a temporal Go/No-Go alternation task, suggesting either an involvement of this medial prefrontal subregion in sequencing temporally ordered behaviors or alternatively in more general response selection processes 'Gisquet-Verrier et al., Psychobiology 28 (2000) 248'. In the present study, the effects of ACd lesions were investigated in two different training situations. Both tasks involved response selection but only one of the two tasks required behavioral sequencing. In experiment 1, rats with ACd lesions were normally able to select Go and No-Go responses, when selection processes were based on a tone/light conditional rule that does not require temporal patterning. In experiment 2, ACd-lesioned rats were disrupted during the acquisition of a spatial alternation task that relies on temporal patterning. These results provide further evidence of ACd involvement in behavioral sequencing, regardless of the nature (spatial or non-spatial) of chained responses. A comparison of ACd lesions-induced effects with those obtained with lesions to the adjacent prelimbic-infralimbic area 'Delatour & Gisquet-Verrier, Behav. Neurosci. 110 (1996) 1282; Delatour & Gisquet-Verrier, Behav. Neurosci. 113 (1999) 941' reveals a double dissociation of these two regions that reflects a functional regionalization of the medial prefrontal cortex in the rat.

Animals↗

PubMed1994

Protein three-dimensional structure determination and sequence-specific assignment of 13C and 15N-separated NOE data. A novel real-space ab initio approach.

The sequence-specific assignment of resonances is considered to be a requirement for the determination of the three-dimensional (3D) structure of a protein in solution by nuclear magnetic resonance methods. The main source of structural information is the nuclear Overhauser effect spectroscopy (NOESY) spectrum, which contains information about spatially close pairs of protons. Currently, various J-correlated spectra must be recorded in order to obtain the sequence-specific assignments necessary to interpret the NOESY spectra. In this work, a novel procedure to determine the 3D structure and the sequence-specific assignments of a protein using only data from 13C and 15N-separated multidimensional NOESY spectra is described. No information from J-correlated spectra is required. The algorithm is called ANSRS (Assignment of NOESY Spectra in Real Space) and is based on an inversion of the traditional strategy. A 3D real-space structure of detected, but unassigned, 1H spins is calculated from the nuclear Overhauser effect (NOE) distance restraints using a dynamical simulated annealing procedure. The sequence-specific assignments are then determined by searching among the 1H spins in the 3D real-space structure for plausible residue assignments. The search uses a Monte Carlo simulated annealing algorithm based on assignment probabilities derived from the 1H, 15N and 13C chemical shifts, various spatial constraints, and the known sequence of the protein. The procedure has been tested on semi-synthetic data sets comprising published experimental chemical shifts and NOE distance restraints derived from the known 3D structures of the two proteins GAL4 (residues 9 to 41) and bovine pancreatic trypsin inhibitor. The ANSRS procedure was able to determine the sequence-specific assignments for more than 95% of the spins, and was fairly robust with respect to missing NOE data. The potential of the ANSRS approach with respect to automated assignment, reduction of the number of NMR spectra required for a structure determination, assignment of homologous and mutant proteins, and the possibility of analysing spectra recorded at high pH is discussed.

Algorithms↗

PubMed2004

Cerebellar stroke impairs temporal but not spatial accuracy during implicit motor learning.

OBJECTIVE: Numerous studies have demonstrated cerebellar activity during implicit motor learning, but few have addressed its specific role. The purpose of this study was to determine if specific components (spatial or temporal) of an implicit motor-tracking task were affected by cerebellar stroke. METHODS: The authors studied the performance of individuals with unilateral cerebellar stroke (n = 7)and a control group (n = 10) across 3 acquisition days and at a delayed retention test as they practiced a unimanual tracking task with the contralesional upper extremity. RESULTS: After cerebellar stroke, participants demonstrated reduced tracking errors for repeating sequences compared to random sequences; however, decomposition of tracking performance into temporal and spatial components revealed persistent deficits in tracking time lag despite improved spatial accuracy. A lesion analysis showed that the dentate nucleus was the only common region affected by all cerebellar strokes. CONCLUSIONS: During implicit motor learning, the cerebellum appears to participate in the formation of predictive strategies for the timing of motor responses, rather than for the accuracy of motor execution. Because deficits were found in the contralesional upper extremity, the authors suggest that this function is not lateralized to 1 hemisphere; cerebellar output may affect the formation of an internal model for timing movements in both upper extremities.

Adult↗

PubMed1986

5'-flanking sequence required for regulated expression of a muscle-specific Drosophila melanogaster actin gene.

We have functionally tested derivatives of a muscle-specific Drosophila melanogaster actin gene in which 5'-flanking sequences have been deleted or rearranged. From our results we conclude that approximately 1,000 nucleotides of 5'-flanking sequence are required for wild-type levels of mRNA accumulation during flight muscle development. Derivatives having 875 or 865 nucleotides of upstream sequence could be expressed normally, but were prone to influence by flanking foreign DNA sequences. Derivatives retaining 600 or fewer nucleotides of flanking DNA did not direct detectable levels of mRNA accumulation. The sequence residing between -919 and -640 could be inverted and yet retain normal function. Deletion of this sequence reduced mRNA accumulation markedly, but did not affect its spatial localization, suggesting that elements which confer tissue specificity reside close to the point of transcription initiation.

Actins↗

PubMed1991

Characterisation of the murine Hox-3.3 gene and its promoter.

The murine Hox-3.3 homeobox containing gene and its Xenopus homologue (XlHbox 1) produce two embryonic transcripts from two distinct promoters located approximately 9 kb apart. In order to begin to characterise one of these promoter regions (PRII), we have sequenced 3 kb of DNA immediately upstream of the transcription start site of the PRII transcript and analyzed the sequence for sequences known to bind transcription factors. Within this region are located a number of sequences that match known cis-elements. We have analysed the ability of two of these sequences that match to the Drosophila hunchback and Antennapedia/fushi-tarazu consensus binding sequences to specifically bind proteins extracted from embryos and from adult tissues. Using gel retention assays with oligonucleotides derived from these sequences, we show that both sequences specifically bind proteins present in extracts of mouse embryos and some, but not all extracts of various adult tissues. Protein binding cannot, however, be correlated with the known spatial domains of Hox-3.3 expression, suggesting that binding to these sequences is not simply related to activation of Hox-3.3 expression. A two base pair change in the most conserved region of the hunchback-like binding sequence completely abolishes protein binding. The presence of these highly conserved cis-acting elements that are known to be involved in regulation of the hunchback, even-skipped and engrailed genes in Drosophila suggests that these sequences may also be involved in the regulation of expression of Hox-3.3 and furthermore that regulation may in part at least involve binding of hunchback-like proteins (i.e. zinc-finger proteins) and Antennapedia-like homeobox-containing proteins.

Amino Acid Sequence↗

PubMed2006

Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments.

A power-law distribution of the length of perfectly conserved sequence from mouse/human whole-genome intersection and alignment is exhibited. Spatial correlations of these elements within the mouse genome are studied. It is argued that these power-law distributions and correlations are comprised in part by functional noncoding sequence and ought to be accounted for in estimating the statistical significance of apparent sequence conservation. These inter-genomic correlations of conservation are placed in the context of previously observed intra-genomic correlations, and their possible origins and consequences are discussed.

Animals↗

PubMed2002

Profiling patterned transcripts in Drosophila embryos.

Here we describe a high-throughput screen to isolate transcripts with spatially restricted patterns of expression in early embryos. Our approach utilizes robotic automation for rapid analysis of sequence-selected cDNAs in a whole-mount in situ hybridization assay. We determined the spatial distribution of a random collection of 778 different genes from an embryonic cDNA library and show that a significant fraction of these exhibit patterned profiles of expression. In addition, gene ontology studies revealed groups of gene products exhibiting shared expression patterns, providing new insights into the largely overlooked effector molecules that function in development. As described in this paper, automated hybridization to whole-mount embryos in situ proved to be straightforward and provided us with a very powerful method for the global survey of gene expression in early embryos. From the perspective of biological significance, our finding that many spatially restricted transcripts correspond to loci encoding novel transcripts that have not been previously identified in nearly saturating genetic screens for maternal effect and zygotic lethals is particularly notable.

Animals↗

PubMed2006

Rapid three-dimensional imaging and analysis of the beating embryonic heart reveals functional changes during development.

We report an accurate method for studying the functional dynamics of the beating embryonic zebrafish heart. The fast cardiac contraction rate and the high velocity of blood cells have made it difficult to study cellular and subcellular events relating to heart function in vivo. We have devised a dynamic three-dimensional acquisition, reconstruction, and analysis procedure by combining (1) a newly developed confocal slit-scanning microscope, (2) novel strategies for collecting and synchronizing cyclic image sequences to build volumes with high temporal and spatial resolution over the entire depth of the beating heart, and (3) data analysis and reduction protocols for the systematic extraction of quantitative information to describe phenotype and function. We have used this approach to characterize blood flow and heart efficiency by imaging fluorescent protein-expressing blood and endocardial cells as the heart develops from a tube to a multichambered organ. The methods are sufficiently robust to image tissues within the heart at cellular resolution over a wide range of ages, even when motion patterns are only quasiperiodic. These tools are generalizable to imaging and analyzing other cyclically moving structures at microscopic scales.

Animals↗

PubMed2007

Diagnosis of breast tumors by contrast-enhanced MR imaging: comparison between the diagnostic performance of dynamic enhancement patterns and morphologic features.

PURPOSE: To compare the diagnostic performance of breast lesions by the enhancement patterns and morphologic criteria on magnetic resonance imaging (MRI). MATERIALS AND METHODS: Both T1-weighted 3D gradient-echo sequences with high temporal resolution and high-spatial-resolution MRI were performed on 190 patients with a total of 204 enhancing lesions (144 malignant and 60 benign). The enhancement patterns and morphologic features of each mass and nonmass lesion were analyzed, and the diagnostic performance was compared. RESULTS: The sensitivity and specificity of the morphologic criteria were statistically significantly higher than those of the enhancement patterns (sensitivity: P = 0.0012, specificity: P = 0.0003), and the A(z) values for the three observers were 0.900, 0.919, and 0.900. The diagnostic accuracy of the morphologic criteria for both types of lesions was superior, and the differences were statistically significant (mass: P = 0.0001, nonmass: P = 0.0389). CONCLUSION: The analysis of the morphologic features of enhancing breast lesions alone showed higher diagnostic performance; therefore, signal intensity (SI) time-course data may not be needed to diagnose malignant breast lesions.

Adult↗

PubMed1990

Spatial localization for motion-rejected NMR imaging: SLO-MOTION.

A new method of eliminating NMR image artifacts caused by random or sporadic motion is presented. The method uses only NMR techniques. A combination of a spatial localization method and a standard 2DFT imaging sequence is employed and consequently named SLO-MOTION. Alternatively, the sequence may be used to aid motion artifact reduction by postprocessing methods. The feasibility of the method is demonstrated on a phantom.

Humans↗

PubMed2006

Fast 3D radiofrequency field mapping using echo-planar imaging.

An inhomogeneous radiofrequency (RF) magnetic field is an essential source of error for the quantification of MRI and MRS parameters. To correct for effects of RF inhomogeneities in 3D data sets, it is necessary to have knowledge of the 3D RF distribution in the sample. In this paper a method for fast 3D RF mapping is presented. The method is based on the simultaneous acquisition of a spin echo (SE) and a stimulated echo (STE) using echo-planar imaging (EPI). The acquisition of the 3D RF map using 64 partitions and TR = 500 ms requires 1.5 min. The use of the sequence in vivo is demonstrated by the calculation of the RF maps in the human brain at 3T. The comparison of calculated flip angles with the flip angles obtained by fitting signal behavior in the 3D stimulated-echo acquisition mode (STEAM)-EPI sequence and the analysis of errors due to spatially dependent T(1) values in the brain show that the accuracy of the calculated flip angles in the human brain is about 2 degrees.

Algorithms↗

PubMed2004

Aromatic side-chain interactions in proteins: near- and far-sequence Tyr-X pairs.

In the present study, an extensive analysis of the aromatic Tyr-X interactions is performed on a data set of 593 PDB structures, X being Phe, His, Tyr, and Trp. The nonredundant Tyr-X pairs (2645) were retained and separated by both the residue distance in the sequence and the secondary structures they bridge. Similar to the Phe-X and His-X pairs, the far-sequence Tyr-X pairs (X partner > five apart in the sequence: 74%) show comparable secondary structures and conformers for either type of X partner, in contrast with the near-sequence Tyr-X pairs (26%). As the Phe-X pairs, the near-sequence Tyr-X pairs stabilize secondary structures, mainly the alpha- helices (positions 1, 3, and 4) and the beta-strands (position 2). Like the Phe-X and His-X pairs, most far-sequence Tyr-X pairs (34%) bridge beta-strands and only 11% bridge helices. As for the Phe-X and the His-X pairs, the X partners of the far-sequence Tyr-X pairs are frequently "above" the tyrosine ring with tilted and normal rings, whereas the X partner of the near-sequence Tyr-X pairs gradually moves from the "aside" to the "above" location, together with a progressive decrease of normal and increase of parallel rings, respectively. Unlike the His-X pairs, the interactions of the hetroatom in Tyr-X pairs are only favored with a sequence position +4 and over, owing to the spatial accessibility of the heteroatom.

Amino Acids, Aromatic↗

PubMed1999

Time Correlations in Fluid Transport Obtained by Sequential Rephasing Gradient Pulses.

We present a basic experiment by which the evolution of the displacement probability density (propagator) of static or flowing fluid in N successive time intervals is obtained by single labeling, coupled with multiple rephasing events during the course of a pulsed field-gradient sequence. We term this type of sequence SERPENT: SEquential Rephasing by Pulsed field-gradients Encoding N Time-intervals. Realizations of the SERPENT experiment for the case N = 2 which include spin echo, stimulated echo, and Carr-Purcell pulse sequences are suggested. They have in common a spatial spin-labeling of the initial magnetization by a gradient of area q0, followed by successive rephasing via gradients q1 and q2 at times t = Delta1 and t = Delta2, respectively, where q0 + q1 + q2 = 0. A two-dimensional Fourier transform with respect to q1 and q2 gives directly the joint probability density W2(R1, Delta1; R2, Delta2) for displacements R1 and R2 in times Delta1 and Delta2, respectively. q1 and q2 may be in arbitrary directions. Assuming R1 ||R2, the correlation coefficient rhoR1,R2 then reflects the time-history of the fluctuating velocities. The behavior of the cross moment can be obtained from either a full two-dimensional or a set of one-dimensional SERPENT measurements. Experimental results are presented for water flowing through a bed of packed glass beads. While Delta1 is appropriately chosen to sample the short-time velocity field within the system, increasing Delta2 clearly shows the loss of correlation when the average fluid element displacement exceeds the bead diameter. Copyright 1999 Academic Press.

Journal Article↗

PubMed1994

The role of the right medial temporal lobe in the control of memory-guided saccades.

The role of the hippocampal formation in the control of memory-guided saccades is unclear. We tested two types of memory-guided saccades with short memorization delay in three patients with a lesion affecting the right medial temporal lobe and involving the hippocampal formation. In single memory-guided saccades, testing spatial working memory, the gain of the patient group did not differ from that of an age-matched control group. In contrast, in sequences of memory-guided saccades, testing chronological working memory, there was a marked and significant increase in the percentage of erroneous sequences in patients, compared to controls. These results suggest an important role of the hippocampal formation in the memorization of the chronological order of saccade sequences. In contrast, this structure does not appear to be crucial for spatial working memory, used in single memory-guided saccades.

Aged↗

PubMedDate not supplied

In vivo localized 1H spectroscopy of the rat eye at 7 T: preliminary studies.

Preliminary in vivo proton spectroscopic studies of the posterior chamber of the rat eye have been undertaken at 7 T. The Spatial and Chemical shift encoded Excitation (SPACE) localization sequence was used to acquire signals from 10 microliter voxels and demonstrate the presence of metabolites associated with the vitreous humor, lens, retina, and the optic nerve. Localized T2 and T1 measurements of water in the vitreous humor indicate a relatively fluid environment. Susceptibility maps are used to demonstrate the difficulties of in vivo spectroscopic investigations in the anterior regions of the eye. Comments are made concerning the implications for spectral resolution in these regions.

Animals↗