Paleomagnetic data and K-Ar ages from Mesozoic units of the Santa Marta massif: A preliminary interpretation for block rotation and translations

We report 6 K-Ar ages and paleomagnetic data from 28 sites collected in Jurassic, Lower Cretaceous and Paleocene rocks of the Santa Marta massif, to test previous hypothesis of rotations and translations of this massif, whose rock assemblage differs from other basement-cored ranges adjacent to the Guyana margin. Three magnetic components were identified in this study. A first component has a direction parallel to the present magnetic field and was uncovered in all units (D 352, I = 25.6, k = 57.35, a95 = 5.3, N = 12). A second component was isolated in Cretaceous limestone and Jurassic volcaniclastic rocks (D = 8.8, I = 8.3, k = 24.71, a95 = 13.7, N = 6), and it was interpreted as of Early Cretaceous age. In Jurassic sites with this component, Early Cretaceous K-Ar ages obtained from this and previous studies are interpreted as reset ages. The third component was uncovered in eight sites of Jurassic volcaniclastic rocks, and its direction indicates negative shallow to moderate inclinations and northeastward declinations. K-Ar ages in these sites are of Early (196.5 +/- 4.9 Ma) to early Late Jurassic age (156.6 +/- 8.9 Ma). Due to local structural complexity and too few Cretaceous outcrops to perform a reliable unconformity test, we only used two sites with (1) K-Ar ages, (2) less structural complexity, and (3) reliable structural data for Jurassic and Cretaceous rocks. The mean direction of the Jurassic component is (D = 20.4, I = -18.2, k = 46.9, a95 = 5.1, n = 18 specimens from two sites). These paleomagnetic data support previous models of northward along-margin translations of Grenvillian-cored massifs. Additionally, clockwise vertical-axis rotation of this massif, with respect to the stable craton, is also documented; the sense of rotation is similar to that proposed for the Perija Range and other ranges of the southern Caribbean margin. More data is needed to confirm the magnitudes of rotations and translations. (C) 2009 Elsevier Ltd. All rights reserved.

Markiana nigripinnis (Perugia, 1891) as a putative member of the subfamily Stevardiinae (Characiformes: Characidae): spermatic evidence

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Assessment of first molars sagittal and rotational position in Class II, division 1 malocclusion

OBJECTIVE: This study assessed the anterior-posterior positioning of the upper and lower first molars, and the degree of rotation of the upper first molars in individuals with Class II, division 1, malocclusion. METHODS: Asymmetry I, an accurate device, was used to assess sixty sets of dental casts from 27 females and 33 males, aged between 12 and 21 years old, with bilateral Class II, division 1. The sagittal position of the molars was determined by positioning the casts onto the device, considering the midpalatal suture as a symmetry reference, and then measuring the distance between the mesial marginal ridge of the most distal molar and the mesial marginal ridge of its counterpart. With regard to the degree of rotation of the upper molar, the distance between landmarks on the mesial marginal ridge was measured. Chi-square test with a 5% significance level was used to verify the variation in molars position. Student's t test at 5% significance was used for statistical analysis. RESULTS: A great number of lower molars mesially positioned was registered, and the comparison between the right and left sides also demonstrated a higher number of mesially positioned molars on the right side of both arches. The average rotation of the molars was found to be 0.76 mm and 0.93 mm for the right and left sides, respectively. CONCLUSION: No statistically significant difference was detected between the mean values of molars mesialization regardless of the side and arch. Molars rotation, measured in millimeters, represented ¼ of Class II.

Combined pre- and subtemporal transtentorial approach for epidermoid cysts of the cerebellopontine angle

Objective Epidermoid cysts of the cerebellopontine angle (CPA) can be a surgical challenge for the pediatric neurosurgeon. Ideally, total removal must be achieved; however, occasional adhesions of these tumors to vital neurovascular structures and extension far beyond the midline may preclude their total removal. The aims of this article are to present an alternative surgical approach to these lesions and to provide the rationale for this technique. Material and methods A 16-year-old boy was admitted to our pediatric neurosurgery department with a 1-year history of nonspecific headaches. His neurological examination showed right-sided dysmetria and gait ataxia. Magnetic resonance scans showed a space-occupying lesion on the right CPA with low intensity on T-1-weighted images and high intensity on T-2-weighted images. Results Craniotomy for tumor excision via pre- and subtemporal transtentorial approach was performed disclosing a 3.5 x 3 x 2.8-cm(3) well-encapsulated tumor, which was confirmed to be an epidermoid cyst. The postoperative course was uneventful. Conclusions A combined pre- and subtemporal approach utilizes a wide opening of the tentorium and the option of supratentorial retraction of the cerebellum to provide an excellent angle of approach to CPA lesions involving the anterolateral aspect of the brain stem in children.

Three-dimensional electron microscopy of myriapod hemocyanin, planorbid snail acetylcholine-binding protein and cyanobacterial Vipp1

Three-dimensional electron microscopy (3-D EM) provides a framework for the analysis of large protein quaternary structures. The advantage over the generally higher resolving meth- od of X-ray crystallography is the embedding of the proteins in their physiological environ- ment. However, results of the two methods can be combined to obtain superior structural information. In this work, three different protein types – (i) Myriapod hemocyanin, (ii) vesi- cle-inducing protein in plastids 1 (Vipp1) and (iii) acetylcholine-binding protein (AChBP) – were structurally analyzed by 2-D and 3-D EM and, where possible, functionally interpreted.rnMyriapod hemocyanins have been previously shown to be 6x6-meric assemblies that, in case of Scutigera coleoptrata hemocyanin (ScoHc), show two 3x6-mer planes whith a stag- gering angle of approximately 60°. Here, previously observed structural differences between oxy- and deoxy-ScoHc could be substantiated. A 4° rotation between hexamers of two dif- ferent 3x6-mer planes was measured, which originates at the most central inter-hexamer in- terface. Further information about allosteric behaviour in myriapod hemocyanin was gained by analyzing Polydesmus angustus hemocyanin (PanHc), which shows a stable 3x6-mer and divergent histidine patterns in the inter-hexamer interfaces when compared to ScoHc. Both findings would conclusively explain the very different oxygen binding properties of chilopod and diplopod hemocyanin.rnVipp1 is a protein found in cyanobacteria and higher plants which is essential for thyla- koid membrane function and forms highly variable ring-shaped structures. In the course of this study, the first 3-D analysis of Vipp1 was conducted and yielded reconstructions of six differently sized Vipp1 rings from negatively stained images at resolutions between 20 to 30 Å. Furthermore, mutational analyses identified specific N-terminal amino acids that are essential for ring formation. On the basis of these analyses and previously published results, a hypothetical model of the Vipp1 tertiary and quaternary structure was generated.rnAChBP is a water-soluble protein in the hemolymph of mollusks. It is a structural and functional homologue of the ligand-binding domain of nicotinic acetylcholine receptors. For the freshwater snail Biomphalaria glabrata, we previously described two types of AChBP (BgAChBP1 and BgAChBP2). In this work, a 6 Å 3-D reconstruction of native BgAChBP is presented, which shows a dodecahedral assembly that is unprecedented for an AChBP. Single particle analysis of recombinantely expressed BgAChBP types led to preliminary results show- ing a dodecahedral assembly of BgAChBP1 and a dipentameric assembly of BgAChBP2. This indicates divergent biological functions of the two types.

Short anterior correction of the thoracolumbar/lumbar curve in King 1 idiopathic scoliosis: the behaviour of the instrumented and non-instrumented curves and the trunk balance

This is a retrospective clinical, radiological and patient outcome assessment of 21 consecutive patients with King 1 idiopathic adolescent scoliosis treated by short anterior selective fusion of the major thoracolumbar/lumbar (TL/L) curve. Three-dimensional changes of both curves, changes in trunk balance and rib hump were evaluated. The minimal follow-up was 24 months (max. 83). The Cobb angle of the TL/L curve was 52 degrees (45-67 degrees) with a flexibility of 72% (40-100%). The average length of the main curve was 5 (3-8) segments. An average of 3 (2-4) segments was fused using rigid single rod implants with side-loading screws. The Cobb angle of the thoracic curve was 33 degrees (18-50 degrees) with a flexibility of 69% (29-100%). The thoracic curve in bending was less than 20 degrees in 17 patients, and 20-25 degrees in 4 patients. In the TL/L curve there was an improvement of the Cobb angle of 67%, of the apex vertebral rotation of 51% and of the apex vertebral translation of 74%. The Cobb angle of the thoracic curve improved 29% spontaneously. Shoulder balance improved significantly from an average preoperative imbalance of 14.5-3.1 mm at the last follow-up. Seventy-five percent of the patients with preoperative positive shoulder imbalance (higher on the side of the thoracic curve) had levelled shoulders at the last follow-up. C7 offset improved from a preoperative 19.8 (0-40) to 4.8 (0-18) mm at the last follow-up. There were no significant changes in rotation, translation of the thoracic curve and the clinical rib hump. There were no significant changes in thoracic kyphosis or lumbar lordosis. The average score of the SRS-24 questionnaire at the last follow-up was 91 points (max. 120). We conclude that short anterior selective fusion of the TL/L curve in King 1 scoliosis with a thoracic curve bending to 25 degrees or less (Type 5 according to Lenke classification) results in a satisfactory correction and a balanced spine. Short fusions leave enough mobile lumbar segments for the establishment of global spinal balance. A positive shoulder imbalance is not a contraindication for this procedure. Structural interbody grafts are not necessary to maintain lumbar lordosis.

Myoepithelioma of the cerebellopontine angle: a previously not documented benign salivary gland-type neoplasm within the cranium

Myoepithelioma is a dimorphic neoplasm with contractile-epithelial phenotype, originally interpreted as deriving from, but not actually restricted to the salivary glands. As a novel addition to the list of exquisitely rare intracranial salivary gland-type tumors and tumor-like lesions, we report on an example of myoepithelioma encountered in the left cerebellopontine angle of a 32-year-old male. Clinically presenting with ataxia and dizziness, this extraaxial mass of 4 × 3.5 × 3 cm was surgically resected, and the patient is alive 6 years postoperatively. Histologically, the tumor exhibited a continuum ranging from compact fascicles of spindle cells to epithelial nests and trabeculae partitioned by hyalinized septa, while lacking tubular differentiation. Regardless of architectural variations, there was robust immunoexpression of S100 protein, smooth muscle actin, GFAP, cytokeratin, and vimentin. Cytologic atypia tended to be modest throughout, and the MIB1 labeling index averaged less than 1%. Fluorescent in situ hybridization indicated no rearrangement of the EWSR1 locus. We interpret these results to suggest that myoepithelioma of the posterior fossa - along with related salivary epithelial tumors in this ostensibly incongruous locale - may possibly represent analogous neoplasms to their orthotopic counterparts, ones arising within aberrant salivary anlagen. The presence of the latter lends itself to being mechanistically accounted for by either postulating placodal remnants in the wake of branchial arch development, or linking them to exocrine glandular nests within endodermal cysts. Alternatively, myoepithelioma at this site could be regarded as a non tissue-specific lesion similar to its relatives ubiquitously occurring in the soft parts.

The rotation state of 67P/Churyumov-Gerasimenko from approach observations with the OSIRIS cameras on Rosetta

Aims. Approach observations with the Optical, Spectroscopic, and Infrared Remote Imaging System (OSIRIS) experiment onboard Rosetta are used to determine the rotation period, the direction of the spin axis, and the state of rotation of comet 67P’s nucleus. Methods. Photometric time series of 67P have been acquired by OSIRIS since the post wake-up commissioning of the payload in March 2014. Fourier analysis and convex shape inversion methods have been applied to the Rosetta data as well to the available ground-based observations. Results. Evidence is found that the rotation rate of 67P has significantly changed near the time of its 2009 perihelion passage, probably due to sublimation-induced torque. We find that the sidereal rotation periods P1 = 12.76129 ± 0.00005 h and P2 = 12.4043 ± 0.0007 h for the apparitions before and after the 2009 perihelion, respectively, provide the best fit to the observations. No signs of multiple periodicity are found in the light curves down to the noise level, which implies that the comet is presently in a simple rotation state around its axis of largest moment of inertia. We derive a prograde rotation model with spin vector J2000 ecliptic coordinates λ = 65° ± 15°, β = + 59° ± 15°, corresponding to equatorial coordinates RA = 22°, Dec = + 76°. However, we find that the mirror solution, also prograde, at λ = 275° ± 15°, β = + 50° ± 15° (or RA = 274°, Dec = + 27°), is also possible at the same confidence level, due to the intrinsic ambiguity of the photometric problem for observations performed close to the ecliptic plane.

Predicting bed form roughness: the influence of lee side angle

Flow transverse bedforms (ripples and dunes) are ubiquitous in rivers and coastal seas. Local hydrodynamics and transport conditions depend on the size and geometry of these bedforms, as they constitute roughness elements at the bed. Bedform influence on flow energy must be considered for the understanding of flow dynamics, and in the development and application of numerical models. Common estimations or predictors of form roughness (friction factors) are based mostly on data of steep bedforms (with angle-of-repose lee slopes), and described by highly simplified bedform dimensions (heights and lengths). However, natural bedforms often are not steep, and differ in form and hydraulic effect relative to idealised bedforms. Based on systematic numerical model experiments, this study shows how the hydraulic effect of bedforms depends on the flow structure behind bedforms, which is determined by the bedform lee side angle, aspect ratio and relative height. Simulations reveal that flow separation behind bedform crests and, thus, a hydraulic effect is induced at lee side angles steeper than 11 to 18° depending on relative height, and that a fully developed flow separation zone exists only over bedforms with a lee side angle steeper than 24°. Furthermore, the hydraulic effect of bedforms with varying lee side angle is evaluated and a reduction function to common friction factors is proposed. A function is also developed for the Nikuradse roughness (k s), and a new equation is proposed which directly relates k s to bedform relative height, aspect ratio and lee side angle.

Characterization of a Right Angle Transfer Point in a Fruit Packing Line

Characteristics of the impacts su!ered by the fruit on a transfer point of an experimental fruit packing line were analysed. The transfer is made up by two transporting belts at di!erent heights forming an angle of 903. These transfer points are very common in fruit packing lines, in which fruits receive two impacts: the "rst onto the belt base and the second into the lateral plate. Diferent tests were carried out to study the e!ect of transfer height, velocity, belt structure and padding on the acceleration values recorded by an instrumental sphere (IS 100). Results showed that transfer height and belt structure a!ect mainly impact values on the belt base, and padding a!ects mainly impact values registered for lateral contact. The elect of belt velocity in both impacts is less important when compared to the rest of the variables. Additionally, two powered transfer decelerators were tested at the same point with the aim of decreasing impacts su!ered by the fruit. Comparing impacts registered using these decelerators to those analysed in the first part of the study without decelerators, a high reduction of the impact values was observed.

Evaluation of angle-dependent absorption: Computer simulation and listening test for an objective and subjective evaluation

The aim of this thesis is the subjective and objective evaluation of angledependent absorption coefficients. As the assumption of a constant absorption coefficient over the angle of incidence is not always held, a new model acknowledging an angle-dependent reflection must be considered, to get a more accurate prediction in the sound field. The study provides information about the behavior of different materials in several rooms, depending on the reflection modeling of incident sound waves. An objective evaluation was run for an implementation of angle-dependent reflection factors in the image source and ray tracing simulation models. Results obtained were analysed after comparison to diffuse-field averaged data. However, changes in acoustic characteristics of a room do not always mean a variation in the listener’s perception. Thus, additional subjective evaluation allowed a comparison between the different results obtained with the computer simulation and the response from the individuals who participated in the listening test. The listening test was designed following a three-alternative forced-choice (3AFC) paradigm. In each interaction asked to the subjects a sequence of either three pink noise bursts or three natural signals was alternated. These results were supposed to show the influence and perception of the two different ways to implement surface reflection –either with diffuse or angle-dependent absorption properties. Results show slightly audible effects when material properties were exaggerated. El objetivo de este trabajo es la evaluación objetiva y subjetiva del coeficiente de absorción en función del ángulo de incidencia de la onda de sonido. La suposición de un coeficiente de absorción constante con respecto al ángulo de incidencia no siempre se sostiene. Por ello, un nuevo modelo considerando la reflexión dependiente del ángulo se debe tener en cuenta para obtener predicciones más certeras en el campo del sonido. El estudio proporciona información sobre el comportamiento de diferentes materiales en distintos recintos, dependientes del modelo de reflexión de las ondas de sonido incidentes. Debido a las dificultades a la hora de realizar las medidas y, por lo tanto, a la falta de datos, los coeficientes de absorción dependientes del ángulo a menudo no se tienen en cuenta a la hora de realizar las simulaciones. Hoy en día, aún no hay una tendencia de aplicar el coeficiente de absorción dependiente del ángulo para mejorar los modelos de reflexión. Por otra parte, para una medición satisfactoria de la absorción dependiente del ángulo, sólo hay unos pocos métodos. Las técnicas de medición actuales llevan mucho tiempo y hay algunos materiales, condiciones y ángulos que no pueden ser reproducidos y, por lo tanto, no es posible su medición. Sin embargo, en el presente estudio, los ángulos de incidencia de las ondas de sonido son conocidos y almacenados en una de base de datos para cada uno de los materiales, de modo que los coeficientes de absorción para el ángulo dado pueden ser devueltos siempre que sean requeridos por el usuario. Para realizar el estudio se llevó a cabo una evaluación objetiva, por medio de la implementación del factor de reflexión dependiente del ángulo en los modelos de fuentes imagen y trazado de rayos. Los resultados fueron analizados después de ser comparados con el promedio de los datos obtenidos en medidas en el campo difuso. La simulación se hizo una vez se configuraron un número de materiales creados por el autor, a partir de los datos existentes en la literatura y los catálogos de fabricantes. Los modelos de Komatsu y Mechel sirvieron como referencia para los materiales porosos, configurando la resistividad al aire o el grosor, y para los paneles perforados, introduciendo el radio de los orificios y la distancia entre centros, respectivamente. Estos materiales se situaban en la pared opuesta a la que se consideraba que debía alojar a la fuente sonora. El resto de superficies se modelaban con el mismo material, variando su coeficiente de absorción y/o de dispersión. Al mismo tiempo, una serie de recintos fueron modelados para poder reproducir distintos escenarios de los que obtener los resultados. Sin embargo, los cambios en las características acústicas de un recinto no significan variaciones en la percepción por parte del oyente. Por ello, una evaluación subjetiva adicional permitió una comparación entre los diferentes resultados obtenidos mediante la simulación informática y la respuesta de los individuos que participaron en la prueba de escucha. Ésta fue diseñada bajo las pautas del modelo de test three-alternative forced-choice (3AFC), con treinta y dos preguntas diferentes. En cada iteración los sujetos fueron preguntados por una secuencia alterna entre tres señales, siendo dos de ellas iguales. Éstas podían ser tanto ráfagas de ruido rosa como señales naturales, en este test se utilizó un fragmento de una obra clásica interpretada por un piano. Antes de contestar al cuestionario, los bloques de preguntas eran ordenados al azar. Para cada ensayo, la mezcla era diferente, así los sujetos no repetían la misma prueba, evitando un sesgo por efectos de aprendizaje. Los bloques se barajaban recordando siempre el orden inicial, para después almacenar los resultados reordenados. La prueba de escucha fue realizada por veintitrés personas, toda ellas con conocimientos dentro del campo de la acústica. Antes de llevar a cabo la prueba de escucha en un entorno adecuado, una hoja con las instrucciones fue facilitada a cada persona. Los resultados muestran la influencia y percepción de las dos maneras distintas de implementar las reflexiones de una superficie –ya sea con respecto a la propiedad de difusión o de absorción dependiente del ángulo de los materiales. Los resultados objetivos, después de ejecutar las simulaciones, muestran los datos medios obtenidos para comprender el comportamiento de distintos materiales de acuerdo con el modelo de reflexión utilizado en el caso de estudio. En las tablas proporcionadas en la memoria se muestran los valores del tiempo de reverberación, la claridad y el tiempo de caída temprana. Los datos de las características del recinto obtenidos en este análisis tienen una fuerte dependencia respecto al coeficiente de absorción de los diferentes materiales que recubren las superficies del cuarto. En los resultados subjetivos, la media de percepción, a la hora de distinguir las distintas señales, por parte de los sujetos, se situó significativamente por debajo del umbral marcado por el punto de inflexión de la función psicométrica. Sin embargo, es posible concluir que la mayoría de los individuos tienden a ser capaces de detectar alguna diferencia entre los estímulos presentados en el 3AFC test. En conclusión, la hipótesis de que los valores del coeficiente de absorción dependiente del ángulo difieren es contrastada. Pero la respuesta subjetiva de los individuos muestra que únicamente hay ligeras variaciones en la percepción si el coeficiente varía en intervalos pequeños entre los valores manejados en la simulación. Además, si los parámetros de los materiales acústicos no son exagerados, los sujetos no perciben ninguna variación. Los primeros resultados obtenidos, proporcionando información respecto a la dependencia del ángulo, llevan a una nueva consideración en el campo de la acústica, y en la realización de nuevos proyectos en el futuro. Para futuras líneas de investigación, las simulaciones se deberían realizar con distintos tipos de recintos, buscando escenarios con geometrías irregulares. También, la implementación de distintos materiales para obtener resultados más certeros. Otra de las fases de los futuros proyectos puede realizarse teniendo en cuenta el coeficiente de dispersión dependiente del ángulo de incidencia de la onda de sonido. En la parte de la evaluación subjetiva, realizar una serie de pruebas de escucha con distintos individuos, incluyendo personas sin una formación relacionada con la ingeniería acústica.

The lipid bilayer determines helical tilt angle and function in lactose permease of Escherichia coli

The structure of lactose permease from Escherichia coli in its lipid environment was studied by attenuated total reflection Fourier transform infrared spectroscopy. The protein exhibits an α-helical content of about 65% and about 25% β-sheet. Unusually fast hydrogen/deuterium (H/D) exchange to 90–95% completion suggests a structure that is highly accessible to the aqueous phase. An average tilt angle of 33° for the helices was found with respect to the bilayer normal at a lipid-to-protein ratio of ≈800:1 (mol/mol), and the permease exhibits optimal activity under these conditions. However, upon decreasing the lipid-to-protein ratio, activity decreases continuously in a manner that correlates with the decrease in the lipid order parameter and the increase in the average helical tilt angle. Taken together, the data indicate that the structure and function of the permease are strongly dependent on the order and integrity of the lipid bilayer.

Absence of a barrier to backwards rotation of the bacterial flagellar motor demonstrated with optical tweezers

A cell of the bacterium Escherichia coli was tethered covalently to a glass coverslip by a single flagellum, and its rotation was stopped by using optical tweezers. The tweezers acted directly on the cell body or indirectly, via a trapped polystyrene bead. The torque generated by the flagellar motor was determined by measuring the displacement of the laser beam on a quadrant photodiode. The coverslip was mounted on a computer-controlled piezo-electric stage that moved the tether point in a circle around the center of the trap so that the speed of rotation of the motor could be varied. The motor generated ≈4500 pN nm of torque at all angles, regardless of whether it was stalled, allowed to rotate very slowly forwards, or driven very slowly backwards. This argues against models of motor function in which rotation is tightly coupled to proton transit and back-transport of protons is severely limited.

Solution structure of the 2-amino-1- methyl-6-phenylimidazo[4,5-b]pyridine C8-deoxyguanosine adduct in duplex DNA

The carcinogenic heterocyclic amine (HA) 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is formed during the cooking of various meats. To enable structure/activity studies aimed at understanding how DNA damaged by a member of the HA class of compounds can ultimately lead to cancer, we have determined the first solution structure of an 11-mer duplex containing the C8-dG adduct formed by reaction with N-acetoxy-PhIP. A slow conformational exchange is observed in which the PhIP ligand either intercalates into the DNA helix by denaturing and displacing the modified base pair (main form) or is located outside the helix in a minimally perturbed B-DNA duplex (minor form). In the main base-displaced intercalation structure, the minor groove is widened, and the major groove is compressed at the lesion site because of the location of the bulky PhIP-N-methyl and phenyl ring in the minor groove; this distortion causes significant bending of the helix. The PhIP phenyl ring interacts with the phosphodiester-sugar ring backbone of the complementary strand and its fast rotation with respect to the intercalated imidazopyridine ring causes substantial distortions at this site, such as unwinding and bulging-out of the strand. The glycosidic torsion angle of the [PhIP]dG residue is syn, and the displaced guanine base is directed toward the 3′ end of the modified strand. This study contributes, to our knowledge, the first structural information on the biologically relevant HA class to a growing body of knowledge about how conformational similarities and differences for a variety of types of lesions can influence protein interactions and ultimately biological outcome.

Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity.

We present an analysis that synthesizes information on the sequence, structure, and motifs of antigenic peptides, which previously appeared to be in conflict. Fourier analysis of T-cell antigenic peptides indicates a periodic variation in amino acid polarities of 3-3.6 residues per period, suggesting an amphipathic alpha-helical structure. However, the diffraction patterns of major histocompatibility complex (MHC) molecules indicate that their ligands are in an extended non-alpha-helical conformation. We present two mutually consistent structural explanations for the source of the alpha-helical periodicity, based on an observation that the side chains of MHC-bound peptides generally partition with hydrophobic (hydrophilic) side chains pointing into (out of) the cleft. First, an analysis of haplotype-dependent peptide motifs indicates that the locations of their defining residues tend to force a period 3-4 variation in hydrophobicity along the peptide sequence, in a manner consistent with the spacing of pockets in the MHC. Second, recent crystallographic determination of the structure of a peptide bound to a class II MHC molecule reveals an extended but regularly twisted peptide with a rotation angle of about 130 degrees. We show that similar structures with rotation angles of 100-130 degrees are energetically acceptable and also span the length of the MHC cleft. These results provide a sound physical chemical and structural basis for the existence of a haplotype-independent antigenic motif which can be particularly important in limiting the search time for antigenic peptides.