The Dimorphos ejecta plume properties revealed by LICIACube.

The Double Asteroid Redirection Test (DART) had an impact with Dimorphos (a satellite of the asteroid Didymos) on 26 September 20221. Ground-based observations showed that the Didymos system brightened by a factor of 8.3 after the impact because of ejecta, returning to the pre-impact brightness 23.7 days afterwards2. Hubble Space Telescope observations made from 15 minutes after impact to 18.5 days after, with a spatial resolution of 2.1 kilometres per pixel, showed a complex evolution of the ejecta3, consistent with other asteroid impact events. The momentum enhancement factor, determined using the measured binary period change4, ranges between 2.2 and 4.9, depending on the assumptions about the mass and density of Dimorphos5. Here we report observations from the LUKE and LEIA instruments on the LICIACube cube satellite, which was deployed 15 days in advance of the impact of DART. Data were taken from 71 seconds before the impact until 320 seconds afterwards. The ejecta plume was a cone with an aperture angle of 140 ± 4 degrees. The inner region of the plume was blue, becoming redder with increasing distance from Dimorphos. The ejecta plume exhibited a complex and inhomogeneous structure, characterized by filaments, dust grains and single or clustered boulders. The ejecta velocities ranged from a few tens of metres per second to about 500 metres per second.

Collisional formation of top-shaped asteroids and implications for the origins of Ryugu and Bennu.

Asteroid shapes and hydration levels can serve as tracers of their history and origin. For instance, the asteroids (162173) Ryugu and (101955) Bennu have an oblate spheroidal shape with a pronounced equator, but contain different surface hydration levels. Here we show, through numerical simulations of large asteroid disruptions, that oblate spheroids, some of which have a pronounced equator defining a spinning top shape, can form directly through gravitational reaccumulation. We further show that rubble piles formed in a single disruption can have similar porosities but variable degrees of hydration. The direct formation of top shapes from single disruption alone can explain the relatively old crater-retention ages of the equatorial features of Ryugu and Bennu. Two separate parent-body disruptions are not necessarily required to explain their different hydration levels.

The solar nebula origin of (486958) Arrokoth, a primordial contact binary in the Kuiper Belt.

The New Horizons spacecraft's encounter with the cold classical Kuiper Belt object (486958) Arrokoth (provisional designation 2014 MU69) revealed a contact-binary planetesimal. We investigated how Arrokoth formed and found that it is the product of a gentle, low-speed merger in the early Solar System. Its two lenticular lobes suggest low-velocity accumulation of numerous smaller planetesimals within a gravitationally collapsing cloud of solid particles. The geometric alignment of the lobes indicates that they were a co-orbiting binary that experienced angular momentum loss and subsequent merger, possibly because of dynamical friction and collisions within the cloud or later gas drag. Arrokoth's contact-binary shape was preserved by the benign dynamical and collisional environment of the cold classical Kuiper Belt and therefore informs the accretion processes that operated in the early Solar System.

Amino acid preferences for specific locations at the ends of alpha helices.

A definition based on alpha-carbon positions and a sample of 215 alpha helices from 45 different globular protein structures were used to tabulate amino acid preferences for 16 individual positions relative to the helix ends. The interface residue, which is half in and half out of the helix, is called the N-cap or C-cap, whichever is appropriate. The results confirm earlier observations, such as asymmetrical charge distributions in the first and last helical turn, but several new, sharp preferences are found as well. The most striking of these are a 3.5:1 preference for Asn at the N-cap position, and a preference of 2.6:1 for Pro at N-cap + 1. The C-cap position is overwhelmingly dominated by Gly, which ends 34 percent of the helices. Hydrophobic residues peak at positions N-cap + 4 and C-cap - 4.

Collisions and gravitational reaccumulation: forming asteroid families and satellites.

Numerical simulations of the collisional disruption of large asteroids show that although the parent body is totally shattered, subsequent gravitational reaccumulation leads to the formation of an entire family of large and small objects with dynamical properties similar to those of the parent body. Simulations were performed in two different collisional regimes representative of asteroid families such as Eunomia and Koronis. Our results indicate that all large family members must be made of gravitationally reaccumulated fragments; that the post-collision member size distribution and the orbital dispersion are steeper and smaller, respectively, than for the evolved families observed today; and that satellites form frequently around family members.

De novo design, expression, and characterization of Felix: a four-helix bundle protein of native-like sequence.

The protein Felix was designed de novo to fold into an antiparallel four-helix bundle of specific topology. Its sequence of 79 amino acid residues is not homologous to any known protein sequence, but is "native-like" in that it is nonrepetitive and contains 19 of the 20 naturally occurring amino acids. Felix has been expressed from a synthetic gene cloned in Escherichia coli, and the protein has been purified to homogeneity. Physical characterization of the purified protein indicates that Felix (i) is monomeric in solution, (ii) is predominantly alpha-helical, (iii) contains a designed intramolecular disulfide bond linking the first and fourth helices, and (iv) buries its single tryptophan in an apolar environment and probably in close proximity with the disulfide bond. These physical properties rule out several alternative structures and indicate that Felix indeed folds into approximately the designed three-dimensional structure.

Preliminary X-ray diffraction studies of acyl carrier protein from Escherichia coli.

Crystals of the acyl carrier protein of Escherichia coli have been grown and analyzed by X-ray diffraction. The crystals grow in space group C2 with unit cell dimensions a = 46.8 A, b = 52.1 A, c = 47.3 A and beta = 93.2 degrees. An isomorphous derivative, HgCl2, has been identified and characterized.

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation.

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 A resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln "flips", this process included rotation of OH, SH, NH3+, and methionine methyl H atoms, flip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide flips (or N and C identity for His flips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 degrees flip to optimize H-bonding and/or to avoid NH2 clashes with neighboring atoms (incorporating a conservative score penalty which, for marginal cases, favors the assignment in the original coordinate file). The programs Reduce, Probe, and Mage provide not only a suggested amide orientation, but also a numerical score comparison, a categorization of the marginal cases, and a direct visualization of all relevant interactions in both orientations. Visual examination allowed confirmation of the raw score assignment for about 40 % of those Asn/Gln flips placed within the "marginal" penalty range by the automated algorithm, while uncovering only a small number of cases whose automated assignment was incorrect because of special circumstances not yet handled by the algorithm. It seems that the H-bond and the atomic-clash criteria independently look at the same structural realities: when both criteria gave a clear answer they agreed every time. But consideration of van der Waals clashes settled many additional cases for which H-bonding was either absent or approximately equivalent for the two main alternatives. With this extra information, 86 % of all side-chain amide groups could be oriented quite unambiguously. In the absence of further experimental data, it would probably be inappropriate to assign many more than this. Some of the remaining 14 % are ambiguous because of coordinate error or inadequacy of the theoretical model, but the great majority of ambiguous cases probably occur as a dynamic mix of both flip states in the actual protein molecule. The software and the 100 coordinate files with all H atoms added and optimized and with amide flips corrected are publicly available.

Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms.

The technique of small-probe contact dot surfaces is described as a method for calculating and displaying the detailed atomic contacts inside or between molecules. It allows one both to measure and to visualize directly the goodness-of-fit of packing interactions. It requires both highly accurate structures and also the explicit inclusion of all hydrogen atoms and their van der Waals interactions. A reference dataset of 100 protein structures was chosen on the basis of resolution (1.7 A or better), crystallographic R-value, non-homology, and the absence of any unusual problems. Hydrogen atoms were added in standard geometry and, where needed, with rotational optimization of OH, SH, and NH+3 positions. Side-chain amide orientations were corrected where required by NH van der Waals clashes, as described in the accompanying paper. It was determined that, in general, methyl groups pack well in the default staggered conformation, except for the terminal methyl groups of methionine residues, which required rotational optimization. The distribution of serious clashes (i.e. non-H-bond overlap of >/=0.4 A) was studied as a function of resolution, alternate conformations, and temperature factor (B), leading to the decision that packing and other structural features would not be analyzed for residues in 'b' alternate conformations or with B-factors of 40 or above. At the level of the fine details analyzed here, structural accuracy improves quite significantly over the range from 1.7 to 1.0 A resolution. These high-resolution structures show impressively well-fitted packing interactions, with some regions thoroughly interdigitated and other regions somewhat sparser. Lower-resolution structures or model structures could undoubtedly be improved in accuracy by the incorporation of this additional information: for example, nucleic acid structures in non-canonical conformations are often very accurate for the bases and much less reliable for the backbone, whose conformation could be specified better by including explicit H atom geometry and contacts. The contact dots are an extremely sensitive method of finding problem areas, and often they can suggest how to make improvements. They can also provide explanations for structural features that have been described only as empirical regularities, which is illustrated by showing that the commonest rotamer of methionine (a left-handed spiral, with all chi values near -60 degrees) is preferred because it provides up to five good H atom van der Waals contacts. This methodology is thus applicable in two different ways: (1) for finding and correcting errors in structure models (either experimental or theoretical); and (2) for analyzing interaction patterns in the molecules themselves.

The kinemage: a tool for scientific communication.

A "kinemage" (kinetic image) is a scientific illustration presented as an interactive computer display. Operations on the displayed kinemage respond within a fraction of a second: the entire image can be rotated in real time, parts of the display can be turned on or off, points can be identified by selecting them, and the change between different forms can be animated. A kinemage is prepared and specified by the author(s) of a journal article, in order to better communicate ideas that depend on three-dimensional information. The kinemages are distributed as plain text files of commented display lists and accompanying explanations. They are viewed and explored in an open-ended way by the reader using a simple graphics program, such as the one described here (called MAGE), which presently runs on Macintosh computers. A utility (called PREKIN) helps authors prepare the kinemages. Kinemages are being implemented under the auspices of the Innovative Technology Fund.

Exploring steric constraints on protein mutations using MAGE/PROBE.

When planning a mutation to test some hypothesis, one crucial question is whether the new side chain is compatible with the existing structure; only if it is compatible can the interpretation of mutational results be straightforward. This paper presents a simple way of using the sensitive geometry of all-atom contacts (including hydrogens) to answer that question. The interactive MAGE/PROBE system lets the biologist explore conformational space for the mutant side chain, with an interactively updated kinemage display of its all-atom contacts to the original structure. The Autobondrot function in PROBE systematically explores that same conformational space, outputting contact scores at each point, which are then contoured and displayed. These procedures are applied here in two types of test cases, with known mutant structures. In ricin A chain, the ability of a neighboring glutamate to rescue activity of an active-site mutant is modeled successfully. In T4 lysozyme, six mutations to Leu are analyzed within the wild-type background structure, and their Autobondrot score maps correctly predict whether or not their surroundings must shift significantly in the actual mutant structures; interactive examination of contacts for the conformations involved explains which clashes are relieved by the motions. These programs are easy to use, are available free for UNIX or Microsoft Windows operating systems, and should be of significant help in choosing good mutation experiments or in understanding puzzling results.

The tyrosine corner: a feature of most Greek key beta-barrel proteins.

The Tyr corner is a conformation in which a tyrosine (residue "Y") near the beginning or end of an antiparallel beta-strand makes an H bond from its side-chain OH group to the backbone NH and/or CO of residue Y - 3, Y - 4, or Y - 5 in the nearby connection. The most common "classic" case is a delta 4 Tyr corner (more than 40 examples listed), in which the H bond is to residue Y - 4 and the Tyr chi 1 is near -60 degrees. Y - 2 is almost always a glycine, whose left-handed beta or very extended beta conformation helps the backbone curve around the Tyr ring. Residue Y - 3 is in polyproline II conformation (often Pro), and residue Y - 5 is usually a hydrophobic (often Leu) that packs next to the Tyr ring. The consensus sequence, then, is LxPGxY, where the first x (the H-bonding position) is hydrophilic. Residues Y and Y - 2 both form narrow pairs of beta-sheet H-bonds with the neighboring strand. delta 5 Tyr corners have a 1-residue insertion between the Gly and Tyr, forming a beta-bulge. One protein family has a delta 4 corner formed by a His rather than a Tyr, and several examples use Trp in place of Tyr. For almost all these cases, the protein or domain is a Greek key beta-barrel structure, the Tyr corner ends a Greek key connection, and it is well-conserved in related proteins. Most low-twist Greek key beta-barrels have 1 Tyr corner. "Reverse" delta 4 Tyr corners (H bonded to Y + 4) and other variants are described, all less common and less conserved. It seems likely that the more classic Tyr corners (delta 4, delta 5, and delta 3 Tyr, Trp, or His) contribute to the stability of a Greek key connection over a hairpin connection, and also that they may aid in the process of folding up Greek key structures.

Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system.

We describe a new paradigm for modeling proteins in interactive computer graphics systems--continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions. Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrange-multiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded beta-ribbon into an approximate beta-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and (2) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed.

The Alacoil: a very tight, antiparallel coiled-coil of helices.

The Alacoil is an antiparallel (rather than the usual parallel) coiled-coil of alpha-helices with Ala or another small residue in every seventh position, allowing a very close spacing of the helices (7.5-8.5 A between local helix axes), often over four or five helical turns. It occurs in two distinct types that differ by which position of the heptad repeat is occupied by Ala and by whether the closest points on the backbone of the two helices are aligned or are offset by half a turn. The aligned, or ROP, type has Ala in position "d" of the heptad repeat, which occupies the "tip-to-tip" side of the helix contact where the C alpha-C beta bonds point toward each other. The more common offset, or ferritin, type of Alacoli has Ala in position "a" of the heptad repeat (where the C alpha-C beta bonds lie back-to-back, on the "knuckle-touch" side of the helix contact), and the backbones of the two helices are offset vertically by half a turn. In both forms, successive layers of contact have the Ala first on one and then on the other helix. The Alacoil structure has much in common with the coiled-coils of fibrous proteins or leucine zippers: both are alpha-helical coiled-coils, with a critical amino acid repeated every seven residues (the Leu or the Ala) and a secondary contact position in between. However, Leu zippers are between aligned, parallel helices (often identical, in dimers), whereas Alacoils are between antiparallel helices, usually offset, and much closer together. The Alacoil, then, could be considered as an "Ala anti-zipper." Leu zippers have a classic "knobs-into-holes" packing of the Leu side chain into a diamond of four residues on the opposite helix; for Alacoils, the helices are so close together that the Ala methyl group must choose one side of the diamond and pack inside a triangle of residues on the other helix. We have used the ferritin-type Alacoil as the basis for the de novo design of a 66-residue, coiled helix hairpin called "Alacoilin." Its sequence is: cmSPDQWDKE AAQYDAHAQE FEKKSHRNng TPEADQYRHM ASQY QAMAQK LKAIANQLKK Gsetcr (with "a" heptad positions underlined and nonhelical parts in lowercase), which we will produce and test for both stability and uniqueness of structure.

Radiotherapy prior to cortical allograft limb sparing in dogs with osteosarcoma: a dose response assay.

Twenty-one dogs with spontaneously occurring appendicular osteosarcoma were given preoperative radiation therapy prior to a limb sparing procedure using a cortical allograft. Radiation doses were randomly assigned, ranged from 36-52 Gy in 4 Gy intervals, and were given in 10 equally-sized fractions on a M, W, F schedule. Seventeen of the 21 dogs underwent the limb sparing procedure approximately 3 weeks after completion of radiation therapy. Local tumor recurrence was documented in 4 of 17 dogs at mean and median times of 5.5 and 5.8 months, respectively, after initiation of radiation therapy. Three of 4 recurrences were in anatomic regions with sparse adjacent soft tissue which precluded wide excision. Complications were significant. Fixation device failure occurred in 9 of 17 dogs and was associated with host bone necrosis, muscle thinning and fibrosis of vessels and nerves in irradiated normal tissue. Incidence of host bone necrosis was directly related to radiation dose (Kendall's statistic, p = 0.005). Metastasis occurred in all 21 dogs. Mean and median times to metastasis in these dogs were 5.1 and 4.0 months, respectively, after initiation of radiation therapy. Local tumor control rates and survival times were higher in dogs developing allograft infection suggesting that infection acted as an immunostimulant. All local failures occurred in dogs that did not develop allograft infection and median survival times for uninfected versus infected dogs were 5 and 11 months, respectively (logrank test, p = 0.029). Increased tumor radiopacity following radiation therapy was significantly related to survival. Median survival in dogs whose tumors were characterized by decreased, unchanged or increased opacity after radiation therapy were 3.5 and 14 months, respectively (logrank test, p = 0.014). Based on the results of our study, radiation therapy can not be recommended as part of limb sparing treatments for patients with osteosarcoma at doses and dose per fraction values similar to those used herein.

Inhibition of arabinose 5-phosphate isomerase. An approach to the inhibition of bacterial lipopolysaccharide biosynthesis.

Arabinose 5-phosphate ( A5P ) isomerase is a key enzyme in the biosynthesis of lipopolysaccharide, an essential component of the outer membrane of Gram-negative bacteria. The mechanism of the isomerase is envisioned to involve an enediol intermediate. A series of compounds, which are analogues of the substrates or intermediate, were tested as inhibitors of A5P isomerase with the belief that a good inhibitor would stop bacterial growth or render the cells more susceptible to other antibiotics or natural defenses. In a series of phosphorylated sugars, the order of isomerase inhibitory activity was as follows: aldonic acids greater than alditols greater than aldoses. Nonphosphorylated sugars were much less inhibitory. The best inhibitor was erythronic acid 4-phosphate (54), which had Km/Ki = 29. None of the compounds displayed antibacterial activity in vitro.

Atypical Menkes steely hair disease.

Menkes steely hair disease (MSHD) is a rare disorder which typically results in severe mental retardation and death in early childhood. A 21-month-old boy with an atypical milder form was presented by Procopis et al. [1981]. A second child with the atypical form is presented here who has survived to age 9 years and is doing well clinically.

Representation, space and Hollywood Squares: looking at things that aren't there anymore.

It has been argued that the human cognitive system is capable of using spatial indexes or oculomotor coordinates to relieve working memory load (Ballard, D. H., Hayhoe, M. M., Pook, P. K., & Rao, R. P. N. (1997). Behavioral and Brain Sciences, 20(4), 723), track multiple moving items through occlusion (Scholl, D. J., & Pylyshyn, Z. W. (1999). Cognitive Psychology, 38, 259) or link incompatible cognitive and sensorimotor codes (Bridgeman, B., & Huemer, V. (1998). Consciousness and Cognition, 7, 454). Here we examine the use of such spatial information in memory for semantic information. Previous research has often focused on the role of task demands and the level of automaticity in the encoding of spatial location in memory tasks. We present five experiments where location is irrelevant to the task, and participants' encoding of spatial information is measured implicitly by their looking behavior during recall. In a paradigm developed from Spivey and Geng (Spivey, M. J., & Geng, J. (2000). submitted for publication), participants were presented with pieces of auditory, semantic information as part of an event occurring in one of four regions of a computer screen. In front of a blank grid, they were asked a question relating to one of those facts. Under certain conditions it was found that during the question period participants made significantly more saccades to the empty region of space where the semantic information had been previously presented. Our findings are discussed in relation to previous research on memory and spatial location, the dorsal and ventral streams of the visual system, and the notion of a cognitive-perceptual system using spatial indexes to exploit the stability of the external world.

Nonelectric laparoscopic sterilization. Experience with a silastic band.

In an attempt to avoid the serious complications of electrosurgical sterilization via laparoscopy, specially designed applicators have been used to apply a silastic band to the fallopian tube, thereby occluding it. Two hundred and eighty cases have been performed, 70 of which have been followed for more than 1 year. There have been no pregnancies. The technic is relatively simple. Complications result when the tube is excessively thickened, when the tube is fixed in position by adhesion, or when the tube is grasped too close to the cornua or too rapidly. These complications have been relatively few and can be easily avoided.

Ischemic necrosis of cartilage in spontaneous and experimental lesions of osteochondrosis.

This study was designed to examine the association of spontaneous lesions of osteochondrosis with vascular supply to epiphyseal cartilage, and to determine whether similar lesions could be experimentally reproduced by selective interruption of cartilage canal blood supply. The vascular supply to the articular-epiphyseal cartilage complex of the distal end of the femur was studied in 27 microfil- or barium-injected and cleared specimens and 24 serially sectioned microangiographic specimens from 27 clinically normal female swine (3.6 to 71.0 kg). Blood vessels supplying the articular-epiphyseal cartilage complex were consistently restricted to the epiphyseal region and the number of vessels decreased as the pigs increased in weight (p less than 0.001). Spontaneous lesions of osteochondrosis (i.e., cartilage necrosis) were initially seen in the first areas of epiphyseal cartilage to become avascular and were associated with necrotic blood vessels. The number and size of foci of necrotic cartilage increased as the pigs increased in weight (p less than 0.001). Blood supply to epiphyseal cartilage from cartilage canal vessels was surgically interrupted in a highly vascular area of the medial femoral condyle in eight additional 23-kg female swine. This procedure resulted in necrosis of blood vessels within cartilage canals followed by necrosis of surrounding cartilage, lesions that appeared to be identical to early spontaneous lesions of osteochondrosis. These results suggest that the viability of epiphyseal cartilage in the articular-epiphyseal cartilage complex is highly dependent on an adequate blood supply from cartilage canal vessels, and strongly implicates a defect in blood supply in the pathogenesis of osteochondrosis.