Silo discharge of binary granular mixtures

We present numerical and experimental results on the mass flow rate during the discharge of three-dimensional silos filled with a bidisperse mixture of grains of different sizes. We analyzed the influence of the ratio between coarse and fine particles on the profile of volume fraction and velocity across the orifice. By using numerical simulations, we have shown that the velocity profile has the same shape as that in the monodisperse case and is insensitive to the composition of the mixture. On the contrary, the volume fraction profile is strongly affected by the composition of the mixture. Assuming that an effective particle size can be introduced to characterize the mixture, we have shown that previous expression for the mass flow rate of monodisperse particles can be used for binary mixtures. A comparison with Beverloo's correlation is also presented.

Relaxation dynamics of tryptophan in water: A UV fluorescence up-conversion and molecular dynamics study

We report on an ultrafast experimental and simulations study of the early relaxation events of photoexcited tryptophan in water. Experimentally, we used fluorescence up-conversion in both polychromatic and single wavelength detection modes in the 300-480 nm range with polarization dependence. We report on the time evolution of the Stokes shift, bandwidth, and anisotropy from tens of femtoseconds to picoseconds. These observables contain signatures of the simultaneous occurrence of intramolecular and solvent-molecule interactions, which we disentangle with the help of nonequilibrium molecular dynamics simulations. We also observe a breakdown of the linear response approximation to describe our results.

Solubilization and characterization of a cell wall-bound trehalase from ascospores of the fission yeast Schizosaccharomyces pombe

The genome of the fission yeast Schizosaccharomyces pombe lacks sequence homologs to ath1 genes coding for acid trehalases in other yeasts or filamentous fungi. However, acid trehalase activity is present at the spore stage in the life cycle of the fission yeast. The enzyme responsible for this activity behaves as a surface enzyme covalently linked to the spore cell walls in both wild-type and ntp1 mutant strains devoid of neutral trehalase. Lytic treatment of particulated cell wall fractions allowed the solubilization of the enzyme into an active form. We have characterized this soluble enzyme and found that its kinetic parameters, optimum pH and temperature, thermal denaturation and salt responses are closely similar to other conventional acid trehalases. Hence, this rather unusual enzyme can be recognized as acid trehalase by its biochemical properties although it does not share genetic homology with other known acid trehalases. The potential role of such acid trehalase in the mobilization of trehalose is discussed.

Treatment of cerebral aneurysms with hydrogel-coated platinum coils (HydroCoil): early single-center experience

PURPOSE

The authors report their experience using HydroCoils in the treatment of cerebral aneurysms.

METHODS

We performed a retrospective review of the first 100 nonrandomized patients (104 coiled saccular cerebral aneurysms) treated with HydroCoils during a 27-month period.

RESULTS

The average percentage of HydroCoil by length detached in treated aneurysms was 45.5% (range, 9.9-100%). Immediate postprocedure angiography demonstrated complete aneurysm occlusion in 34%, neck remnant in 35%, and incomplete occlusion in 32%. Immediate procedure-related morbidity and mortality rates were 5.8% and 0%, respectively. Angiographic follow-up was obtained in 51% (51/100 patients; 53/104 aneurysms; average, 10.3 months; range, 0-31 months). In these 53 angiographically followed aneurysms, the overall recanalization rate was 21%: no recanalization occurred in 23 aneurysms with small size (<10 mm)/small neck (<4 mm) (S/S); 4 recanalizations occurred in 7 aneurysms with small size/wide neck (>4 mm) (S/W); 6 recanalizations (27%) occurred in 22 large (L) aneurysms (>10-25 mm, 70% angiographic follow-up); and 1 giant (G) (>25 mm) aneurysm recanalized. A large proportion of aneurysms that were not initially completely occluded were completely occluded on follow-up (15/43 [35%]). Clinical follow-up was obtained in 73 patients (73%; average, 5.3 months; range, 0-24 months): 93% of these patients were neurologically improved or unchanged. Three patients rehemorrhaged and 3 patients with unruptured aneurysms developed delayed hydrocephalus.

CONCLUSIONS

The overall safety profile of HydroCoils appears acceptable. Preliminary midterm observations suggest less coil compaction/aneurysm recanalization in large aneurysms. However, HydroCoil-related delayed hydrocephalus is a concern.

Molecular dynamics of HIV-1 reverse transcriptase indicates increased flexibility upon DNA binding

HIV-1 reverse transcriptase (RT) is one of the main targets for drugs used in the treatment of AIDS, among them, the non-nucleoside RT inhibitors (NNRTIs). The flexibility of RT unliganded and complexed to double-stranded DNA (RT/dsDNA), in water, has been studied by means of molecular dynamics. The simulations show that RT flexibility depends on its ligation state. The RT/dsDNA trajectories show larger fluctuations in the atomic positions than uncomplexed RT, particularly at the tips of the p66 fingers and thumb subdomains. This increased flexibility is consistent with the ability of the p66 fingers of the RT/dsDNA complex to close down after the binding of a deoxynucleoside triphosphate (dNTP) molecule, as observed in the crystal structures of RT/dsDNA bound to dNTP. The two complexation states present different patterns of concerted motions, indicating that the bound dsDNA alters RT flexibility. The motions of amino acid residues that form the non-nucleoside RT inhibitor binding pocket upon complexation with a NNRTI are anticorrelated with the p66 fingers (in RT/dsDNA) and correlated to the RNase H subdomain (unliganded RT). These concerted motions indicate that binding of a NNRTI could alter the flexibility of the subdomains whose motions are correlated to those of the binding pocket.

Perfusion brain scintigraphy studies in infants and children with malformations of the vein of Galen

Cerebral perfusion brain scintigraphy obtained in six unselected patients (age newborn to 14 years) from among 50 children with vein of Galen malformations was used in conjunction with magnetic resonance imaging to determine the basis of the neurological and cognitive abnormalities in patients with vein of Galen malformations (VGMs). Five had a hemiparesis - persistent, transient, or alternating. Four were developmentally delayed. Two had so far been cognitively normal and acquired a neurological deficit, following an embolization procedure. The school age patient had a nonverbal learning disability. Three had epilepsy and/or an abnormal electroencephalogram. Magnetic resonance imaging documented only the VGM, hydrocephalus and atrophy; one child with perinatal asphyxia had periventricular leukomalacia. Perfusion brain scintigraphy was normal in two (a normal infant, and a toddler with a hemiparesis and aphasia). Abnormal findings included: left parietal hypoperfusion, fronto-temporal atrophy, patchy flow; left fronto-temporal hypoperfusion, left hemiatrophy, bilateral medial temporal hypoperfusion, right cerebellar hypoperfusion; right temporal hypoperfusion, patchy flow; right hemiatrophy, occipital hypoperfusion. Perfusion brain scintigraphy findings correlated better with focal neurological and cognitive defects than did magnetic resonance imaging.

Long-term maturation of visual pathways

Previous research in adults has demonstrated the utility of the visual evoked potential (VEP) to measure the integrity of the chromatic and achromatic visual pathways. The VEP has also been shown to be a valuable indicator of maturation of these pathways in infants up to 1 year of age. The present manuscript reports changes in the visual pathways from 2 years to adulthood as measured by the spatio-chromatic VEP. The responses to achromatic reversal stimuli designed to preferentially activate the low spatial-frequency achromatic (luminance) pathways appear adult-like by 1 year of age. The responses to low spatial-frequency isoluminant onset stimuli designed to preferentially activate the chromatic pathway do not appear as they do in the adult until after 12-13 years of age. The shapes of the chromatic VEP waveforms shift from a positive-negative complex to a negative-positive complex. These changes can be modeled by a decrease in the latency of a large negative component between the ages of 1 year and adulthood. The results suggest that for low spatial-frequency stimuli, there are long-term changes in the development of the chromatic pathways that are not observed in the low spatial-frequency achromatic pathways. The changes in the chromatic VEP waveforms with age may be a physiological correlate of reported behavioral changes.

Major subdomain rearrangement in HIV-1 reverse transcriptase simulated by molecular dynamics

We have performed eight 1-ns in vacuo molecular dynamics simulations of HIV-1 reverse transcriptase (RT). Starting with the p66 thumb subdomain in an upright configuration, the p66 thumb moved down over the palm during six of the eight trajectories, in excellent agreement with the crystallographic structure of unliganded RT. The large rearrangement of the p66 thumb subdomain, its tip moving approximately 30 A, occurs during the first 30-200 ps. This approach may allow a detailed study of the processes involved in biologically significant conformational changes in macromolecules.

[Cyclosporosis. Report of a clinical case in Concepción, Chile]

Cyclospora cayetanensis is a newly recognized parasite widely distributed throughout the world, and isolated from children, immunocompetent adults and HIV infected individuals. The clinical manifestations of the infection are watery prolonged diarrhea, anorexia, fatigue, nausea, bloating and weight loss. In immunocompetent individuals, diarrhea is usually self limited but may last several weeks. In immunocompromised hosts it is prolonged, severe and can be associated with biliary tract involvement. We report a 50 years old female that, five days after returning from Cuba, presented with low grade fever, anorexia, fatigue, explosive diarrhea and weight loss. Physical examination was normal. A stool specimen contained many organisms with morphological features of Cyclospora caetanensis. The diagnosis was confirmed at the Centers for Disease Control (Atlanta Ga).

[Hospital nursing conducted according to Rogers' theory. The participating process of human field patterning in a clinical environment]

The participating process of human field patterning in an acute-care environment Scientific story-telling is the basis of this article, which describes the care of a patient within the conceptual framework of Martha Rogers. Dr. Mary Madrid, a nurse at New York University Hospital and a student of Rogers, describes the continuous process of intentional pattern changes of the human energy field. The human energy field finds itself in an ongoing, mutual and integral process with the environmental energy field. Madrid elucidates in this way that the human energy field is integral to a continuous, mutual process of becoming and enfolding with the universe. The theory of Barrett, derived from Rogers' "Science of unitary human beings" is applied. Furthermore, nursing interventions congruent with Rogers' system are being described. These are therapeutic touch, guided visualisation, music therapy as well as breathing and relaxation exercises. This scientific story of Madrid is an excellent example of Rogers' science-based nursing.

Occipital arteriovenous malformations: visual disturbances and presentation

BACKGROUND

Occipital arteriovenous malformations (AVMs) cause a variety of visual disturbances and headaches. Early diagnosis may lead to treatment that reduces the risk of hemorrhages, visual field loss and other neurologic deficits, and death.

METHODS

We reviewed the records of the 70 patients with occipital AVMs referred to New York University Medical Center to investigate the mode of presentation and the outcome of treatment.

RESULTS

Sixty-eight patients presented with one or more symptoms, including homonymous visual disturbances in 39, headache in 39, seizures in 20, and hemorrhage in twenty-six. Visual field loss was more common (p = 0.0007) and more severe (p = 0.0002) in patients who bled than in those with unruptured AVMs (16/44). The frequency of visual field loss was not associated with calcarine artery supply to the AVM. Prior to treatment, the fields improved in five patients with visual loss associated with a hemorrhage. Forty-six patients were treated with embolization, surgery, radiosurgery, or a combination of therapies. The AVM was eliminated in 19 of 20 patients (nine with preoperative partial embolization) treated with surgery versus in 4 of 27 patients treated only with embolization. There were two AVM-associated deaths, two subarachnoid hemorrhages, and four new neurologic deficits after treatment. Visual fields were worse in 15 patients, unchanged in 22, and improved in eight.

CONCLUSIONS

Whereas some features of headache and visual symptoms are similar for occipital AVMs and migraine, the two disorders are usually distinguishable. Visual field improvement can spontaneously occur in patients who have had loss secondary to an intracerebral bleed. Treatment with embolization or surgery, particularly with surgical excision of the AVM, can result in new or worse visual field loss.

A novel low oxygen affinity recombinant hemoglobin (alpha96val--> Trp): switching quaternary structure without changing the ligation state

Using our Escherichia coli expression plasmid (pHE2) in which synthetic human alpha and beta-globin genes are coexpressed with the E. coli methionine aminopeptidase gene under the control of separate tac promoters, we have constructed a new artificial hemoglobin in which the valine residue at position 96 of the alpha chain, located in the alpha 1 beta 2 subunit interface, has been replaced by a tryptophan residue using site-directed mutagenesis. We have determined the oxygen-binding properties of this recombinant hemoglobin, r Hb (alpha 96Val-->Trp), and have used proton nuclear magnetic resonance spectroscopy to investigate its tertiary structure around the heme group and the quaternary structure in the alpha 1 beta 2 subunit interface. This artificial hemoglobin shows a low oxygen affinity, but high cooperativity in oxygen binding, and exhibits no unusual subunit dissociation when ligated. Molecular dynamics simulations suggest that the unique oxygen-binding property of r Hb (alpha 96Val-->Trp) may be due to an extra hydrogen bond between alpha 96Trp and beta 99Asp in the alpha 1 beta 2 subunit interface in the deoxy form. Despite the replacement of a small amino acid residue, valine, by a large tryptophan residue in the alpha 1 beta 2 subunit interface, this artificial hemoglobin shows very similar tertiary structure around the heme pockets and quaternary structure in the alpha 1 beta 2 subunit interface compared to those of human normal adult hemoglobin. Another unique feature of this artificial hemoglobin is that the ligated form, e.g. carbonmonoxy form, of this hemoglobin in the oxy-quaternary structure can be converted to the deoxy-like quaternary structure by the addition of an allosteric effector, inositol hexaphosphate, as well as by lowering the temperature in the absence of inositol hexaphosphate, without changing its ligation state. Thus, this recombinant hemoglobin can be used to gain new insights regarding the nature of subunit interactions in the alpha 1 beta 2 interface and the molecular basis for the allosteric mechanism of hemoglobin.

Deep central arteriovenous malformations of the brain: the role of endovascular treatment

Cerebral deep central arteriovenous malformations (AVMs) are uncommon lesions associated with considerable difficulty in treatment. The authors report a series of 14 deep central AVMs treated by endovascular methods and examine the present role of endovascular treatment. This treatment used alone resulted in complete obliteration of AVMs in approximately 15% of case and reduction in 50% to a size permitting treatment by means of radiosurgery. Reversal of previous neurological signs and symptoms occurred in 35.7% of embolized patients. Overall, nearly 80% of patients had either complete obliteration of the lesion, reduction to a size allowing radiosurgical treatment, or reversal of previous neurological deficits. There were treatment complications in 14.3% of the cases. Endovascular treatment methods may make a significant contribution to the therapy of AVMs that have a particularly poor course and are difficult to treat by other means.

Restoring allosterism with compensatory mutations in hemoglobin

Abnormal human hemoglobins (HBs) with amino acid substitutions in the alpha 1 beta 2 interface have very high oxygen affinity and greatly reduced cooperativity in O2 binding compared to normal human Hb. In such abnormal Hbs with mutations at position beta 99, the intersubunit hydrogen bonds between Asp-beta 99 and Tyr-alpha 42 and between Asp-beta 99 and Asn-alpha 97 are broken, thus destabilizing the deoxyquaternary structure of these Hbs. A molecular dynamics method has been used to design compensatory amino acid substitutions in these Hbs that can restore their allosteric properties. We have designed a compensatory mutation in a naturally occurring mutant Hb, Hb Kempsey (Asp-beta 99-->Asn), and have produced it using our Escherichia coli expression plasmid pHE2. We have determined the O2 binding properties of this recombinant double mutant Hb, Hb(Asp-beta 99-->Asn and Tyr-alpha 42-->Asp) and have used 1H NMR spectroscopy to investigate the tertiary structures around the heme groups and the quaternary structure in the alpha 1 beta 2 subunit interface. Our results clearly show that the Tyr-alpha 42-->Asp replacement can substantially compensate for the functional defect of Hb Kempsey caused by the Asp-beta 99-->Asn substitution. The structural and functional information derived from this recombinant Hb provides insights into the structural basis of allosterism and the design of compensatory amino acid substitutions to restore the functional properties of other abnormal HBs associated with hemoglobinopathies.

Sinus venosus atrial septal defect associated with vein of Galen malformations: report of two cases

Two unique cases are presented of infants with signs of vein of Galen malformations, whose unsuspected associated sinus venosus atrial septal defects were detected during routine echocardiography. A conservative approach to cardiac treatment is advocated.

Recent improvement in outcome using transcatheter embolization techniques for neonatal aneurysmal malformations of the vein of Galen

Vein of Galen malformations may present as congestive heart failure in the neonate and are usually fatal if untreated. Early studies using transcatheter embolization techniques, in a series of 22 patients, had a 50% mortality rate and a 37% incidence of severe mental retardation in survivors. Modifications of embolization techniques and neonatal care have improved the outlook in a more recent series of 11 patients. The diagnosis was established within 3 days of life in 91% of the cases. No mortality occurred, and 6 of the patients were functionally normal at up to 30 months' follow-up. Although two patients had severe neurologic deficits and/or a seizure disorder, only one case was possibly temporally associated with the embolization procedure. Some developmental delay was noted in one other patient. These improvements result, in part, from modifications of the treatment protocol, including earlier diagnosis, avoidance of digoxin, improvement in the application of newer microcatheters and acrylic polymers (n-butylcyanoacrylate), avoidance of overly aggressive neurosurgical procedures, and the use of stable central vascular access for total parenteral nutrition accompanying other general improvements in neonatal care.

Reconstruction of the ligated external carotid artery for embolization of cervicofacial arteriovenous malformations

PURPOSE

Until recently, the accepted management of life-threatening complications of unresectable cervicofacial arteriovenous malformations (AVMs) has been ligation of the major feeding vessels, usually the branches or the main trunk of the external carotid artery. Rapid enlargement of collateral vessels around the ligature is usually associated with an early return of symptoms. Percutaneous transcatheter embolization of the nidus of the arteriovenous malformation is now the preferred treatment for symptomatic AVMs that cannot be excised. Previous ligation of the main feeding vessels prevents catheter access and embolization therapy of the lesion. The purpose of this report is to describe our experience with the treatment of patients with symptomatic unresectable cervicofacial AVMs and previous external carotid artery ligation.

METHODS

Six patients with symptoms from cervicofacial arteriovenous malformations required surgical reconstruction of their previously ligated external carotid artery with the anticipation of catheter embolization therapy to the branch vessels feeding the malformation. Saphenous vein was used in five reconstructions; a polytetrafluoroethylene graft was used in one.

RESULTS

After successful arterial reconstruction, massive swelling of the tongue and perioral tissue developed in two patients, which necessitated tracheostomy in one patient; and embolization therapy before extubation could be safely performed in the other patient. In all, four patients underwent successful embolization therapy. One refused subsequent treatment. In one patient with severe epistaxis, external carotid artery revascularization led to the healing of the nasal ulcers without need for embolization therapy.

CONCLUSIONS

For patients with previous ligations of the external carotid artery and symptomatic AVMs, revascularization of the external carotid artery is an important step in treatment. The surgery must be carefully coordinated with the interventional radiologist for possible emergency postoperative embolization therapy. External carotid artery ligation only complicates the treatment of patients with cervicofacial AVMs, and should no longer be used in the treatment of these individuals.

Refined solution structure and ligand-binding properties of PDC-109 domain b. A collagen-binding type II domain

We have determined, via 1H-n.m.r., the solution conformation of the collagen-binding b-domain of the bovine seminal fluid protein PDC-109 (PDC-109/b). The structure determination is based on 341 interproton distance estimates and 42 dihedral angle estimates: a set of 24 initial structures were computed; 12 using the variable target function program DIANA, and 12 using the metric matrix program DISGEO. These structures were optimized by restrained energy minimization and dynamic simulated annealing using the CHARMM and X-PLOR programs. The average pairwise root-mean-square difference (r.m.s.d) between the optimized DIANA (DISGEO) structures is 0.71 A (0.82 A) for the backbone atoms, and 1.73 A (2.03 A) for all atoms. Both sets of structures exhibit the same global fold, secondary structure and placement of most non-polar side-chains. Two central antiparallel beta-sheets, which lie roughly perpendicular to each other, and two irregular loops support a large, partially exposed, hydrophobic surface that defines a putative binding site. A test of a hybrid relaxation matrix-based distance refinement protocol (MIDGE program) was performed using a normalized 250 millisecond NOESY spectrum. The resulting distances were input to the molecular mechanics/dynamics procedures mentioned above in order to optimize the DIANA structures. Our results indicate that relaxation matrix refinement of distances is most useful when used conservatively for identifying underestimated distance constraints. 1H-n.m.r. monitored ligand titration experiments revealed definite, albeit weak, binding interactions for phenethylamine and leucine analogs (Ka less than or equal to 25 M-1). Residues perturbed by ligand binding include Tyr7, Trp26, Tyr33, Asp34 and Trp39. These results suggest that PDC-109/b may recognize specific leucine and/or isoleucine-containing sequences within collagen.

Neonatal vein of Galen malformations: experience in developing a multidisciplinary approach using an embolization treatment protocol

A multidisciplinary team approach using a staged transcatheter embolization and neurosurgical protocol was applied to 22 patients with neonatal presentation of vein of Galen malformations over a 12 year period. Aggressive medical therapy was combined with interventions including: ventricular shunting, transcatheter embolization, retrograde transtorcular embolization, and neurosurgical obliteration. There was a high frequency of high output cardiac failure, multiple organ system dysfunction, seizures, hydrocephalus, visual, developmental and neurological disability. Of the first 11 patients, five survived; four with seizures and three with marked retardation. Of the last 11 patients, six survived; five with seizures but only one with retardation. Despite persistently high morbidity and mortality, our continuously evolving protocol offers these otherwise hopeless patients some chance of survival.

Management of facial arteriovenous malformations

Today's management of vascular anomalies requires that the nurse be a vital element in the recovery process. Understanding the role of embolization in managing vascular lesions and keeping informed about the newest developments in this fast changing field enables the nurse to better help the patient toward a successful outcome.

The solution conformations of ferrichrome and deferriferrichrome determined by 1H-NMR spectroscopy and computational modeling

We have applied computational procedures that utilize nmr data to model the solution conformation of ferrichrome, a rigid microbial iron transport cyclohexapeptide of known x-ray crystallographic structure [D. van der Helm et al. (1980) J. Am. Chem. Soc. 102, 4224-4231]. The Al3+ and Ga3+ diamagnetic analogues, alumichrome and gallichrome, dissolved in d6-dimethylsulfoxide (d6-DMSO), were investigated via one- and two-dimensional 1H-nmr spectroscopy at 300, 600, and 620 MHz. Interproton distance constraints derived from proton Overhauser experiments were input to a distance geometry algorithm [T. F. Havel and K. Wüthrich (1984) Bull. Math. Biol. 46, 673-691] in order to generate a family of ferrichrome structures consistent with the experimental data. These models were subsequently optimized through restrained molecular dynamics/energy minimization [B. R. Brooks et al. (1983) J. Comp. Chem. 4, 187-217]. The resulting structures were characterized in terms of relative energies and conformational properties. Computations based on integration of the generalized Bloch equations for the complete molecule, which include the 14N-1H dipolar interaction, demonstrate that the x-ray coordinates reproduce the experimental nuclear Overhauser effect time courses very well, and indicate that there are no significant differences between the crystalline and solution conformations of ferrichrome. A similar study of the metal free peptide, deferriferrichrome, suggests that at least two conformers are present in d6-DMSO at 23 degrees C. Both are different from the ferrichrome structure and explain, through conformational averaging, the observed amide NH and CH alpha multiplet splittings. The occurrence of interconverting peptide backbone conformations yields an increased number of sequential NH-CH alpha and NH-NH Overhauser connectivities, which reflects the mean value of r-6 dependence of the dipolar interaction. Our results support the idea that, in the case of structurally rigid peptides, moderately accurate distance constraints define a conformational subspace encompassing the "true" structure, and that energy considerations reduce the size of this subspace. For flexible peptides, however, the straight-forward approach can be misleading since the nmr parameters are averaged over substantially different conformational states.

[Nuclear magnetic resonance and protein structure]

NMR provides a wealth of structural information about proteins in solution, but does not, by itself, permit an unambiguous determination of a unique structure. A rigorous interpretation of NMR data to obtain the entire family of structures compatible with a given data set requires extensive, systematic and unbiased sampling of the conformational space of the polypeptide chain. Methods of sampling based on the exclusion paradigm--i. e. those that generate structures, check constraints and accept or reject members of the family on that basis, avoid the problem of generating erroneous structures by converging on local minima, which is a common pitfall of methods based on the optimization paradigm. Their much higher computational cost can be reduced by solving the structure in stages, using abstract representations of partial structures, and guiding the computation by control heuristics. The heuristic refinement method developed at Stanford and encoded in the expert system PROTEAN yields more or less extensive families of structures, depending on the size of the NMR data set, and defines the "allowed volume" in which each atom (or other substructure) may lie, with all experimental constraints satisfied. The allowed volume is a measure of the uncertainty of our knowledge of the structure, to which both the limitations of the data and the uncertainty of position resulting from molecular motion may contribute. Prediction of the experimental NMR spectra by solving the generalized Bloch equations (or the Redfield density matrix) for the protein, using atomic coordinates that lie within the allowed atomic volume, provides the final test for the correctness of the proposed structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Comparison of experimentally determined protein structures by solution of Bloch equations

Nuclear Overhauser enhancement (NOESY) spectra were theoretically generated by solving the generalized Bloch equations with the appropriate initial conditions. The input to the equations were the coordinates of the protons of two similar crystal structures of basic pancreatic trypsin inhibitor. The two NOESY spectra obtained were compared to published experimental spectra of the protein in solution. It was found that the two crystal structures of basic pancreatic trypsin inhibitor give different theoretical spectra. The solution of the Bloch equations is very sensitive to small variations in the distance between protons (approx. 0.2 A), and to differences in the surrounding configurations. The method allows a detailed comparison of the crystal and solution structures of proteins. The structure of the trypsin inhibitor in solution was found to be similar to either one or the other crystal forms in different regions of the molecule.