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Background and Purpose: High-resolution vessel wall MR imaging is prone to slow-flow artifacts, particularly when gadolinium shortens the T1 relaxation time of blood. This study aimed to determine the optimal preparation pulses for contrast-enhanced high-resolution vessel wall MR imaging., Materials and Methods: Fifty patients who underwent both motion-sensitized driven equilibrium and delay alternating with nutation for tailored excitation (DANTE) preparation pulses with contrast-enhanced 3D-T1-FSE were retrospectively included. Qualitative analysis was performed using a 4-grade visual scoring system for black-blood performance in the small-sized intracranial vessels, overall image quality, severity of artifacts, and the degree of blood suppression in all cortical veins as well as transverse sinuses. Quantitative analysis of the M1 segment of the MCA was also performed., Results: The qualitative analysis revealed that motion-sensitized driven equilibrium demonstrated a significantly higher black-blood score than DANTE in contrast-enhanced 3D-T1-FSE of the A3 segment (3.90 versus 3.58, P  < .001); M3 (3.72 versus 3.26, P  = .004); P2 to P3 (3.86 versus 3.64, P  = .017); the internal cerebral vein (3.72 versus 2.32, P  < .001); and overall cortical veins (3.30 versus 2.74, P  < .001); and transverse sinuses (2.82 versus 2.38, P  < .001). SNR lumen , contrast-to noise ratio wall-lumen , and SNR wall in the M1 vessel were not significantly different between the 2 preparation pulses (all, P  > .05)., Conclusions: Motion-sensitized driven equilibrium demonstrated improved blood suppression on contrast-enhanced 3D-T1-FSE in the small intracranial arteries and veins compared with DANTE. Motion-sensitized driven equilibrium is a useful preparation pulse for high-resolution vessel wall MR imaging to decrease venous contamination and suppress slow-flow artifacts when using contrast enhancement., (© 2022 by American Journal of Neuroradiology.)

Background and Purpose: Synthetic MR imaging is a time-efficient technique. However, its rather long scan time can be challenging for children. This study aimed to evaluate the clinical feasibility of accelerated synthetic MR imaging with deep learning-based reconstruction in pediatric neuroimaging and to investigate the impact of deep learning-based reconstruction on image quality and quantitative values in synthetic MR imaging., Materials and Methods: This study included 47 children 2.3-14.7 years of age who underwent both standard and accelerated synthetic MR imaging at 3T. The accelerated synthetic MR imaging was reconstructed using a deep learning pipeline. The image quality, lesion detectability, tissue values, and brain volumetry were compared among accelerated deep learning and accelerated and standard synthetic data sets., Results: The use of deep learning-based reconstruction in the accelerated synthetic scans significantly improved image quality for all contrast weightings ( P  < .001), resulting in image quality comparable with or superior to that of standard scans. There was no significant difference in lesion detectability between the accelerated deep learning and standard scans ( P > .05). The tissue values and brain tissue volumes obtained with accelerated deep learning and the other 2 scans showed excellent agreement and a strong linear relationship (all, R 2 > 0.9). The difference in quantitative values of accelerated scans versus accelerated deep learning scans was very small (tissue values, <0.5%; volumetry, -1.46%-0.83%)., Conclusions: The use of deep learning-based reconstruction in synthetic MR imaging can reduce scan time by 42% while maintaining image quality and lesion detectability and providing consistent quantitative values. The accelerated deep learning synthetic MR imaging can replace standard synthetic MR imaging in both contrast-weighted and quantitative imaging., (© 2022 by American Journal of Neuroradiology.)

Objective: The aim of this study was to establish a triaging system for assessment of breast referrals from primary care to ensure safe and effective breast services without compromising breast cancer management., Background: COVID-19 was officially declared a global pandemic on 11 March 2020, and with no effective treatment available, preventing spread has been paramount. Previously, all referrals from primary care were seen in the rapid-access breast clinic (RABC). Clinic appointments exposed patients and healthcare professionals to risk., Method: Initial triage during the lockdown was in line with national governing body guidance, rejected low risk referrals and streamed remaining patients through a telephone consultation to RABC or discharge. A modified triage pathway streamed all patients through virtual triage to RABC, telephone clinic or discharge with advice and guidance categories. Demographics, reasons for referral and outcomes data were collected and presented as median with range and frequency with percentages., Results: Initial triage (23 March-23 April 2020) found fewer referrals with a higher percentage of breast cancer diagnoses. Modified triage (22 June-17 July 2020) resulted in a 35.1% (99/282) reduction in RABC attendance. Overall cancer detection rate remained similar at 4.2% of all referrals pre-COVID (18/429) and 4.3% (12/282) during modified triage. After six months follow-up of patients not seen in RABC during the modified triage pathway, 18 patients were re-referred to RABC and none were diagnosed with cancer., Conclusion: A modified triage pathway has the potential to improve triage efficiency and prevent unnecessary visits during the COVID-19 pandemic. Further refinement of pathway is feasible in collaboration with primary care.

Background and Purpose: The long scan time of MR imaging is a major drawback limiting its clinical use in neuroimaging; therefore, we aimed to investigate the clinical feasibility of a 1-minute full-brain MR imaging using a multicontrast EPI sequence on a different MR imaging scanner than the ones previously reported., Materials and Methods: We retrospectively reviewed the records of 146 patients who underwent a multicontrast EPI sequence, including T1-FLAIR, T2-FLAIR, T2WI, DWI, and T2*WI sequences. Two attending neuroradiologists assessed the image quality of each sequence to compare the multicontrast EPI sequence with routine MR imaging protocols. We used the Wilcoxon signed rank test and McNemar test to compare the 2 MR imaging protocols., Results: The multicontrast EPI sequence generally showed sufficient image quality of >2 points using a 4-point assessment scale. Regarding image quality and susceptibility artifacts, there was no significant difference between the multicontrast EPI sequence DWI and routine DWI ( P  > .05), attesting to noninferiority of the multicontrast EPI, whereas there were significant differences in the other 4 sequences between the 2 MR imaging protocols., Conclusions: The multicontrast EPI sequence showed sufficient image quality for clinical use with a shorter scan time; however, it was limited by inferior image quality and frequent susceptibility artifacts compared with routine brain MR imaging. Therefore, the multicontrast EPI sequence cannot completely replace the routine MR imaging protocol at present; however, it may be a feasible option in specific clinical situations such as screening, time-critical diseases or for use with patients prone to motion., (© 2020 by American Journal of Neuroradiology.)

Background and Purpose: Conventional MR imaging techniques cannot produce optimal images of bone structures because bone has little water and a very short T2 life span. The aim of this study was to investigate the clinical feasibility of skull MR imaging using the zero TE sequence in patients with head trauma by assessing its diagnostic image quality and quantitative measurement compared with CT images., Materials and Methods: Thirteen enrolled patients with head trauma were assessed using brain CT and skull MR imaging. Image quality was graded on a 5-point Likert scale to compare the 2 modalities. To evaluate quantitative analyses between the 2 imaging modalities, we measured skull thickness and normalized bone tissue signal. Interobserver reliability was assessed using weighted κ statistics and the intraclass correlation coefficient., Results: Both imaging techniques clearly depicted skull fractures in all 13 patients. The mean scores for skull MR imaging and CT were 4.65 ± 0.56 and 4.73 ± 0.45 ( P = .157), respectively, with substantial interobserver agreement ( P < .05). The 2 imaging modalities showed no difference in skull thickness ( P = .092) and had good correlation ( r 2 = 0.997). The mean value of normalized bone tissue signal among the 3 layers of the skull was relatively consistent ( P = .401) with high interobserver agreement ( P < .001)., Conclusions: Zero TE skull MR imaging has diagnostic image quality comparable with that of CT images. It also provides consistent results on the quantitative measurement of cortical bone with CT images., (© 2019 by American Journal of Neuroradiology.)

BTG3 (B-cell translocation gene 3) is a p53 target that also binds and inhibits E2F1. Although it connects two major growth-regulatory pathways functionally and is downregulated in human cancers, whether and how BTG3 acts as a tumor suppressor remain largely uncharacterized. Here we present evidence that BTG3 binds and suppresses AKT, a kinase frequently deregulated in cancers. BTG3 ablation results in increased AKT activity that phosphorylates and inhibits glycogen synthase kinase 3β. Consequently, we also observed elevated β-catenin/T-cell factor activity, upregulation of mesenchymal markers, and enhanced cell migration. Consistent with these findings, BTG3 overexpression suppressed tumor growth in mouse xenografts, and was associated with diminished AKT phosphorylation and reduced β-catenin in tissue specimens. Significantly, a short BTG3-derived peptide was identified, which recapitulates these effects in vitro and in cells. Thus, our study provides mechanistic insights into a previously unreported AKT inhibitory pathway downstream of p53. The identification of an AKT inhibitory peptide also unveils a new avenue for cancer therapeutics development.

Introduction: In 2009 the Department of Health instructed McKinsey & Company to provide advice on how commissioners might achieve world class National Health Service productivity. Asymptomatic inguinal hernia repair was identified as a potentially cosmetic procedure, with limited clinical benefit. The Birmingham and Solihull primary care trust cluster introduced a policy of watchful waiting for asymptomatic inguinal hernia, which was implemented across the health economy in December 2010. This retrospective cohort study aimed to examine the effect of a change in clinical commissioning policy concerning elective surgical repair of asymptomatic inguinal hernias., Methods: A total of 1,032 patients undergoing inguinal hernia repair in the 16 months after the policy change were compared with 978 patients in the 16 months before. The main outcome measure was relative proportion of emergency repair in groups before and after the policy change. Multivariate binary logistic regression was used to adjust the main outcome for age, sex and hernia type., Results: The period after the policy change was associated with 59% higher odds of emergency repair (3.6% vs 5.5%, adjusted odds ratio [OR]: 1.59, 95% confidence interval [CI]: 1.03-2.47). In turn, emergency repair was associated with higher odds of adverse events (4.7% vs 18.5%, adjusted OR: 3.68, 95% CI: 2.04-6.63) and mortality (0.1% vs 5.4%, p<0.001, Fisher's exact test)., Conclusions: Introduction of a watchful waiting policy for asymptomatic inguinal hernias was associated with a significant increase in need for emergency repair, which was in turn associated with an increased risk of adverse events. Current policies may be placing patients at risk.

Aim: The National Bowel Cancer Screening Programme (NBCSP) was introduced in the West Midlands in 2006. Studies, including the UK Bowel Cancer Screening Pilot, have reported an 18% reduction in mortality. This regional study assesses the impact of screening on elective and emergency colorectal cancer (CRC) surgery., Method: Data were extracted from the West Midlands cancer registration database for CRC diagnosed in residents of the West Midlands between 1998 and 2010. Screen-detected cancers were identified by matching to the NBCSP database. Mode of admission and intervention was obtained by matching to Hospital Episode Statistics and the classification of Interventions and Procedures code., Results: Of 42,082 patients diagnosed with CRC, 30,309 received surgical treatment. From 1998 to 2005, the number of patients who underwent emergency surgery increased from 4362 to 18,357, with the proportion each year remaining constant (23.85 ± 0.95% each year). In the screening age group (60-69 years) over the same period, emergency surgery was performed in 918 of 4831 patients (19.15 ± 1.65% each year). Following the introduction of screening, the emergency surgery rate decreased each year, reaching 16% (406/2520) in all patients and 12% (101/829) in the screening age group in 2010 (P < 0.001). These changes in emergency surgery were mirrored by increases in elective surgery., Conclusion: The NBCSP has had a positive impact on elective and emergency surgery for CRC in the West Midlands., (Colorectal Disease © 2014 The Association of Coloproctology of Great Britain and Ireland.)

A 61-year-old woman attended the breast clinic with unresolving mastitis and an associated mass, following failed treatment with antibiotics. Triple assessment confirmed idiopathic granulomatous mastitis. Unresponsive to further conservative management and steroid therapy, she underwent surgical excision and made uneventful recovery. No evidence of recurrence was detected at 18 months follow-up.

The Korea Invisible Mass Search (KIMS) experiment presents new limits on the weakly interacting massive particle (WIMP)-nucleon cross section using data from an exposure of 3409 kg.d taken with low-background CsI(Tl) crystals at the Yangyang Underground Laboratory. The most stringent limit on the spin-dependent interaction for a pure proton case is obtained. The DAMA signal region for both spin-independent and spin-dependent interactions for the WIMP masses greater than 20 GeV/c2 is excluded by the single experiment with crystal scintillators.

Sporamin, a sweet potato tuberous storage protein, has trypsin inhibitory activity. Sequence comparison with other plant trypsin inhibitors (TIs) of the Kunitz family reveals that, instead of the conserved Arg or Lys found in other Kunitz TIs, sporamin contains a negatively charged residue (Asp70 or Glu72) at the P1 reactive site. Using site-directed mutagenesis, six mutants were generated containing substitutions at the reactive site and at one of the disulfide bonds, and the recombinant proteins were assayed for TI activity. Mutants Asp70Val and Glu72Arg were found to have only 2-3% of the wild-type activity. These results provide the first evidence for a negatively charged trypsin inhibitory loop and a new mechanism of trypsin inhibition in the Kunitz family.

Previous studies on a limited number of ataxia-telangiectasia (A-T) patients with detectable levels of intracellular ATM protein have suggested a genotype/phenotype correlation. We sought to elucidate this possible correlation by comparing ATM protein levels with mutation types, radiosensitivity, and clinical phenotype. In this study, Western blot analysis was used to measure ATM protein in lysates of lymphoblastoid cell lines (LCLs) from 123 unrelated A-T patients, 10 A-T heterozygotes, and 10 patients with phenotypes similar to A-T. Our Western blot protocol can detect the presence of ATM protein in as little as 1 microg of total protein; at least 25 microg of protein was tested for each individual. ATM protein was absent in 105 of the 123 patients (85%); most of these patients had truncating mutations. The remaining subset of 18 patients (15%) had reduced levels of normal-sized ATM protein; missense mutations were more common in this subset. We used a colony survival assay to characterize the phenotypic response of the LCLs to radiation exposure; patients with or without detectable ATM protein were typically radiosensitive. Nine of 10 A-T heterozygotes also had reduced expression of ATM, indicating that both alleles contribute to ATM protein production. These data suggest that although ATM-specific mRNA is abundant in A-T cells, the abnormal ATM protein is unstable and is quickly targeted for degradation. We found little correlation between level of ATM protein and the type of underlying mutation, the clinical phenotype, or the radiophenotype., (Copyright 2000 Academic Press.)

Abrus agglutinin (AAG), a low-toxicity protein from the plant Abrus precatorius, is less lethal than abrina (ABRa) in mice (LD(50) = 5 mg/kg versus 20 microg/kg of body weight). Nucleotide sequence analysis of a cDNA clone encoding full-length AAG showed an open reading frame with 1641 base pairs, corresponding to a 547-amino acid residue preproprotein containing a signal peptide and a linker region (two amino acid residues) between the AAG-A and AAG-B subunits. AAG had high homology to ABRa (77.8%). The 13 amino acid residues involved in catalytic function, which are highly conserved among abrins and ricins, were also conserved within AAG-A. The protein synthesis inhibitory activity of AAG-A (IC(50) = 3.5 nM) was weaker than that of ABRa-A (0.05 nM). Molecular modeling followed by site-directed mutagenesis showed that Pro(199) of AAG-A, located in amphiphilic helix H and corresponding to Asn(200) of ABRa-A, can induce bending of helix H. This bending would presumably affect the binding of AAG-A to its target sequence, GpApGpAp, in the tetraloop structure of the 28 S rRNA subunit and could be one of the major factors contributing to the relatively weak protein synthesis inhibitory activity and toxicity of AAG.

Territrem B (TRB) is a fungal metabolite isolated from Aspergillus terreus shown previously to be a potent and irreversible inhibitor of acetylcholinesterase (AChE). In the present study, a number of binding and inhibition assays were carried out to further characterize the inhibitory effect of TRB. The results indicate that the binding of TRB (a) is much more selective than a well characterized selective inhibitor of AChE, BW284C51, (b) adopts a one-to-one stoichiometry with the enzyme, (c) cannot be undone by an AChE-regenerating oxime agent, which contrasts the ability of 8 M urea to release AChE-bound TRB, (d) is enhanced by high concentration NaCl but prevented, unless preincubated, by Triton X-100, and (e) exhibits quasi-first order kinetics with an overall inhibition constant of 0.01 nM(-1) min(-1). Together these results suggest a very different irreversible binding (a noncovalent type) from that of the covalent type, which involves typical irreversible AChE inhibitors such as diisopropylfluorophosphate and neostigmine. According to the prediction of a molecular modeling study, the distinct AChE inhibitory characteristics of TRB may arise from the inhibitor being noncovalently trapped within a unique active-site gorge structure of the enzyme. It was predicted that an optimal TRB. AChE binding would position a narrowing connection of the TRB structure at a constricted area near the entrance of the gorge, thereby providing a structural basis for the observed irreversible binding.

The alpha-helical coiled coil motif is among the first characterized and widely found architecture of protein structures. We report here a fast and reliable approach of simulated annealing molecular dynamics (SA/MD) for predicting the three-dimensional structures of various alpha-helical coiled coils of heptad repeat. One key element of our simulation involves a geometric restraint requiring residues occupying the first and fourth positions of the heptad to orient to the angle of their respective statistical average derived from a survey of coiled-coil structures deposited in the Protein Data Bank. Another is the incorporation of subunit rotation and inversion operations for generating symmetrized protein assemblies during the dynamics simulations. The procedure is fully automated and can be applied to different oligomerization states of identical subunits, as well as both parallel and antiparallel arrangements. Despite simplicity, the formation of five coiled-coil prototype systems driven by the restraint-based SA/MD approach shows that the level of prediction accuracy achieved previously by more elaborate procedures can be retained. The present work thus provides validation of a simulation approach that can be employed to utilize a wide variety of knowledge-based geometric restraints for structural prediction of symmetrical or pseudo-symmetrical protein systems., (Copyright 1999 John Wiley & Sons, Inc.)

A crucial element of many gene functions is protein-induced DNA bending. Computer-generated models of such bending have generally been derived by using a presumed bending angle for DNA. Here we describe a knowledge-based docking strategy for modeling the structure of bent DNA recognized by a major groove-inserting alpha-helix of proteins with a helix-turn-helix (HTH) motif. The method encompasses a series of molecular mechanics and dynamics simulations and incorporates two experimentally derived distance restraints: one between the recognition helix and DNA, the other between respective sites of protein and DNA involved in chemical modification-enabled nuclease scissions. During simulation, a DNA initially placed at a distance was "steered" by these restraints to dock with the binding protein and bends. Three prototype systems of dimerized HTH DNA binding were examined: the catabolite gene activator protein (CAP), the phage 434 repressor (Rep), and the factor for inversion stimulation (Fis). For CAP-DNA and Rep-DNA, the root mean square differences between model and x-ray structures in nonhydrogen atoms of the DNA core domain were 2.5 A and 1.6 A, respectively. An experimental structure of Fis-DNA is not yet available, but the predicted asymmetrical bending and the bending angle agree with results from a recent biochemical analysis.

Previous results from our laboratory have shown that phosphorylation of type VI adenylyl cyclase (ACVI) by protein kinase C (PKC) caused suppression of adenylyl cyclase activity. In the present study, we investigated the role of the N terminus cytosolic domain of ACVI in this PKC-mediated inhibition of ACVI. Removal of amino acids 1 to 86 of ACVI or mutation of Ser(10) (a potential PKC phosphorylation site) into alanine significantly relieved the PKC-mediated inhibition and markedly reduced the PKC-evoked protein phosphorylation. PKC also effectively phosphorylated a recombinant N terminus cytosolic domain (amino acids 1-160) protein of ACVI and a synthetic peptide representing Ser(10). In addition, the amino acids 1 to 86 truncated mutant exhibited kinetic properties similar to those of the wild type. Taken together, these data demonstrate that the highly variable N terminus cytoplasmic domain of ACVI is a regulatory domain with a critical role in PKC-mediated suppression, which is a hallmark of this adenylyl cyclase isozyme. In addition, Ser(10) was found to serve as an acceptor for the PKC-mediated phosphorylating transfer of ACVI.

Most enzymes that utilize dinucleotide NAD or NADP are known to comprise a glycine-rich loop segment (e.g. the GXGXXG signature motif of Rossman fold) which binds the cofactor's diphosphate moiety. Through analysis of a set of diverse NAD(P)-bound protein structures, we show here that with few exceptions this diphosphate binding is complemented by a second loop segment interacting from a different angle with unconventional yet apparently ubiquitous C-HellipsisO hydrogen bonds formed between C5' methylene of dinucleotide and, primarily, carbonyl oxygen of protein. This finding implicates an important role of C5' in protein-nucleotide recognition., (Copyright 1998 Academic Press Limited.)

Although the free energy perturbation approach is a rigorous method for estimating the relative binding free energy between an enzyme and its inhibitors, it is computationally expensive. This paper examines the accuracy at different levels of approximations, following the series expansion of free energy derived by Aqvist et al. Level-0 calculates only the enzyme-inhibitor interaction energy at the minimum energy configuration without solvent. In Level-0MD, the inhibitor configurations are sampled by molecular dynamics. These levels assume that the second- and higher order terms in the series expansion can be neglected and that the interaction energies in the bound and unbound states are equal. Level-1 does not assume equal interaction energies in the bound and unbound states. Level-1S includes the solvent contribution but both enzyme and inhibitor are fixed. In Level-1SMD, the inhibitor configurations are sampled by molecular dynamics. Level-2SMD retains the second-order term. We chose seven HIV-1 protease inhibitors for study: A77003, A76889, A76928, A78791, A74704, JG365 and MVT101. Level-0 and Level-0MD were found to give essentially the same relative interaction energies by using the AMBER force field, suggesting that fixing atomic positions may be a good approximation in some cases. However, as expected, Level-0 or Level-0MD gave poor predictions for the relative binding free energies between hydrophobic inhibitors (e.g. A77003) and more hydrophilic inhibitors (e.g. JG365). Level-1SMD produced a much better correlation between calculated and experimental results. Inclusion of the second-order term did not improve the accuracy.

The methodology for deriving class II force fields has been applied to acetal, hemiacetal, and carbohydrate compounds. A set of eighteen model compounds containing one or more anomeric centers was selected for generating the quantum mechanical energy surface, from which the force field was derived and the functional form assessed. The quality of the fit was tested by comparing the energy surface predicted by the force field with ab initio results. Structural, energetic, and dynamic properties (vibrational frequencies) were analyzed. In addition, alpha and beta anomeric equilibrium structures and energies of 2-methoxytetrahydropyran, 2-deoxyribose, and glucose were computed at the HF/6-31G* and higher ab initio levels. These calculations provide test data from molecules outside the training set used to derive the force field. The quantum calculations were used to assess the ability of the class II force field and two quadratic diagonal (class I) force fields, CVFF, and Homans' extension of the AMBER force field, to account for the anomeric effects on the structural and energetic properties of carbohydrate systems. These class I force fields are unable to account for observed structural and energetic trends, exhibiting deviations as large as 5 kcal/mol in relative energies. The class II force field, on the other hand, is shown to reproduce anomeric structural as well as energetic differences. An energy component analysis of this force field shows that the anomeric differences are dominated by torsional energies, although coupling terms, especially angle/torsion, also make significant contributions (roughly 1 kcal/mol in glucose). In addition, the force field accurately accounts for both anomeric and exo-anomeric energy differences in 2-methoxytetrahydropyran, and anomeric energy differences in 2-deoxyribose and glucose.

Motivation: Lacking structures resolved at atomic resolution, the great majority of membrane proteins have typically been depicted in a schematic two-dimensional (2D) topology consisting of putative transmembrane domains predicted from hydropathy plots. As more and more sequences of membrane proteins become available from genome projects, there is a need to automate the process of generating the schematic topology while allowing important information, such as the individual amino acid and the extent to which it is conserved in evolution, to be conveniently inspected. We addressed this need by developing a program called VHMPT., Results: VHMPT (a graphical V iewer and editor for H elical line M embrane P rotein T opologies) can automatically generate a schematic 2D topology for a protein with transmembrane helices. Through an interactive graphical interface, VHMPT allows users to modify the layout of the generated topology, label specific amino acid or amino acid groups, and annotate with arrows and texts. Given a multiple sequence alignment file, VHMPT can also color code a normalized conservation score for each amino acid on the generated topology, allowing ready visual recognition of highly conserved (or variable) topological regions. VHMPT is written in Tcl/Tk and can run on platforms that have installed the Tcl/Tk interpreter., Availability: The source code and a user manual for VHMPT are available for download at http://www. ibms.sinica.edu.tw/mjhwang/vhmpt., Contact: mjhwang@mail.ibms.sinica.edu.tw

Recent studies making use of channel-blocking peptides as molecular calipers have revealed the architecture of the pore-forming region of Shaker-type potassium channels. Here we show that the low-resolution, experimentally derived geometric information can be incorporated as restraints within the context of an annealed molecular dynamics simulation to predict an atomic structure for the channel pore which, by virtue of restraints, conforms to the experimental evidence. The simulation is reminiscent of the computational method employed by nuclear magnetic resonance (NMR) spectroscopists to resolve solution structures of biological macromolecules, but in lieu of restraints conventionally derived from NMR spectra, novel restraints are developed that include side-chain orientation of amino acid residues and assumed symmetry of protein subunits. The method presented here offers the possibility of expanding cooperation between simulation and experiment in developing structural models, especially for systems such as ion channels whose three-dimensional structures may not be amenable to determination by direct methods at the present time.

In this modeling, we show that the elusive Fis N-terminus involved in invertase-mediated site-specific DNA inversion is, by all indications, a hinged flapping loop. The prediction is based on a combined sequence and secondary structure alignment against known structures of protein segments, as well as a tetrapeptide fragment observed crystallographically. Its validity is strongly supported by the ability to interpret consistently the available mutagenesis data pertaining to this region including, especially, a series of deletion mutants which until this work had been a puzzle in the search for structural explanations. A model for Fis-invertase recognition is also proposed.