Protein dynamics with off-lattice Monte Carlo moves

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte Carlo moves are used: single rotations about torsion axes, and cooperative rotations in windows of amide planes, changing the conformation globally and locally, respectively. For local moves Jacobians are used to obtain an unbiased distribution of dihedrals. A molecular dynamics energy function adapted to the protein model is employed. A polypeptide is folded into native-like structures by local but not by global moves.Comment: 10 pages, 4 Postscript figures, uses epsf.sty and a4.sty; scheduled tentatively for Phys.Rev.E issue of 1 March 199

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software

Terahertz underdamped vibrational motion governs protein-ligand binding in solution

Low-frequency collective vibrational modes in proteins have been proposed as being responsible for efficiently directing biochemical reactions and biological energy transport. However, evidence of the existence of delocalized vibrational modes is scarce and proof of their involvement in biological function absent. Here we apply extremely sensitive femtosecond optical Kerr-effect spectroscopy to study the depolarized Raman spectra of lysozyme and its complex with the inhibitor triacetylchitotriose in solution. Underdamped delocalized vibrational modes in the terahertz frequency domain are identified and shown to blue-shift and strengthen upon inhibitor binding. This demonstrates that the ligand-binding coordinate in proteins is underdamped and not simply solvent-controlled as previously assumed. The presence of such underdamped delocalized modes in proteins may have significant implications for the understanding of the efficiency of ligand binding and protein–molecule interactions, and has wider implications for biochemical reactivity and biological function

The First Flight of the Marshall Grazing Incidence X-ray Spectrometer (MaGIXS)

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) sounding rocket experiment launched on July 30, 2021 from the White Sands Missile Range in New Mexico. MaGIXS is a unique solar observing telescope developed to capture X-ray spectral images, in the 6 - 24 Angstrom wavelength range, of coronal active regions. Its novel design takes advantage of recent technological advances related to fabricating and optimizing X-ray optical systems as well as breakthroughs in inversion methodologies necessary to create spectrally pure maps from overlapping spectral images. MaGIXS is the first instrument of its kind to provide spatially resolved soft X-ray spectra across a wide field of view. The plasma diagnostics available in this spectral regime make this instrument a powerful tool for probing solar coronal heating. This paper presents details from the first MaGIXS flight, the captured observations, the data processing and inversion techniques, and the first science results.Comment: 20 pages, 18 figure

A Self-Organizing Algorithm for Modeling Protein Loops

Protein loops, the flexible short segments connecting two stable secondary structural units in proteins, play a critical role in protein structure and function. Constructing chemically sensible conformations of protein loops that seamlessly bridge the gap between the anchor points without introducing any steric collisions remains an open challenge. A variety of algorithms have been developed to tackle the loop closure problem, ranging from inverse kinematics to knowledge-based approaches that utilize pre-existing fragments extracted from known protein structures. However, many of these approaches focus on the generation of conformations that mainly satisfy the fixed end point condition, leaving the steric constraints to be resolved in subsequent post-processing steps. In the present work, we describe a simple solution that simultaneously satisfies not only the end point and steric conditions, but also chirality and planarity constraints. Starting from random initial atomic coordinates, each individual conformation is generated independently by using a simple alternating scheme of pairwise distance adjustments of randomly chosen atoms, followed by fast geometric matching of the conformationally rigid components of the constituent amino acids. The method is conceptually simple, numerically stable and computationally efficient. Very importantly, additional constraints, such as those derived from NMR experiments, hydrogen bonds or salt bridges, can be incorporated into the algorithm in a straightforward and inexpensive way, making the method ideal for solving more complex multi-loop problems. The remarkable performance and robustness of the algorithm are demonstrated on a set of protein loops of length 4, 8, and 12 that have been used in previous studies

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS)

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) is a sounding rocket instrument that flew on July 30, 2021 from the White Sands Missile Range, NM. The instrument was designed to address specific science questions that require differential emission measures of the solar soft X-ray spectrum from 6 – 25[Formula: see text]Å(0.5 – 2.1[Formula: see text]keV). MaGIXS comprises a Wolter-I telescope, a slit-jaw imaging system, an identical pair of grazing incidence paraboloid mirrors, a planar grating and a CCD camera. While implementing this design, some limitations were encountered in the production of the X-ray mirrors, which ended up as a catalyst for the development of a deterministic polishing approach and an improved meteorological technique that utilizes a computer-generated hologram (CGH). The opto-mechanical design approach addressed the need to have adjustable and highly repeatable interfaces to allow for the complex alignment between the optical sub-assemblies. The alignment techniques employed when mounting the mirrors and throughout instrument integration and end-to-end testing are discussed. Also presented are spatial resolution measurements of the end-to-end point-spread-function that were obtained during testing in the X-ray Cryogenic Facility (XRCF) at NASA Marshall Space Flight Center. Lastly, unresolved issues and off-nominal performance are discussed

Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities

The dose response curve is the gold standard for measuring the effect of a drug treatment, but is rarely used in genomic scale transcriptional profiling due to perceived obstacles of cost and analysis. One barrier to examining transcriptional dose responses is that existing methods for microarray data analysis can identify patterns, but provide no quantitative pharmacological information. We developed analytical methods that identify transcripts responsive to dose, calculate classical pharmacological parameters such as the EC50, and enable an in-depth analysis of coordinated dose-dependent treatment effects. The approach was applied to a transcriptional profiling study that evaluated four kinase inhibitors (imatinib, nilotinib, dasatinib and PD0325901) across a six-logarithm dose range, using 12 arrays per compound. The transcript responses proved a powerful means to characterize and compare the compounds: the distribution of EC50 values for the transcriptome was linked to specific targets, dose-dependent effects on cellular processes were identified using automated pathway analysis, and a connection was seen between EC50s in standard cellular assays and transcriptional EC50s. Our approach greatly enriches the information that can be obtained from standard transcriptional profiling technology. Moreover, these methods are automated, robust to non-optimized assays, and could be applied to other sources of quantitative data

The First Flight of the Marshall Grazing Incidence X-Ray Spectrometer (MaGIXS)

The Marshall Grazing Incidence X-ray Spectrometer (MaGIXS) sounding rocket experiment launched on 2021 July 30 from the White Sands Missile Range in New Mexico. MaGIXS is a unique solar observing telescope developed to capture X-ray spectral images of coronal active regions in the 6–24 Å wavelength range. Its novel design takes advantage of recent technological advances related to fabricating and optimizing X-ray optical systems, as well as breakthroughs in inversion methodologies necessary to create spectrally pure maps from overlapping spectral images. MaGIXS is the first instrument of its kind to provide spatially resolved soft X-ray spectra across a wide field of view. The plasma diagnostics available in this spectral regime make this instrument a powerful tool for probing solar coronal heating. This paper presents details from the first MaGIXS flight, the captured observations, the data processing and inversion techniques, and the first science results

Factors influencing accuracy of computer-built models: a study based on leucine zipper GCN4 structure.

A three-dimensional model of the leucine zipper GCN4 built from its amino acid sequence had been reported previously by us. When the two alternative x-ray structures of the GCN4 dimer became available, the root mean square (r.m.s.) shifts between our model and the structures were determined as approximately 2.7 A on all atoms. These values are similar to the r.m.s. shift of 2.8 A between the two GCN4 structures in the different crystal forms (C2 and P2(1)2(1)2(1)). CONGEN conformational searches were run to better understand the conditions that may determine the preference of different conformers in different environments and to test the sensitivity of our current modeling techniques. With a judicious choice of CONGEN search parameters, the backbone r.m.s. deviation improved to 0.8 A and 2.5 A on all atoms. The side-chain conformations of Val and Leu at the helical interface were well reproduced (1.2 A r.m.s.), and the large side-chain misplacements occurred with only a small number of charged amino acids and a tyrosine. Inclusion of the crystal environment (C2 symmetry), as a passive background, into the side-chain conformational search further improved the accuracy of the model to an r.m.s. deviation of 2.1 A. Conformational searches carried out in the two different crystal environments and employing the AMBER protein/DNA forcefield, as implemented in CONGEN, gave the r.m.s. values of 2.2 A (for the C2 symmetry) and 2.5 A (for the P2(1)2(1)2(1) symmetry). In the C2 symmetry crystal, as much as 40% of the surface of each dimer was involved in crystal contacts with other dimers, and the charged residues on the surface often interacted with immobilized water molecules. Thus, occasional large r.m.s. deviations between the model and the x-ray side chains were due to specific conditions that did not occur in solution