Critical assessment of methods of Protein Structure Prediction (CASP) – Round XIII

CASP (Critical Assessment of Structure Prediction) assesses the state of the art in modeling protein structure from amino acid sequence. The most recent experiment (CASP13 held in 2018) saw dramatic progress in structure modeling without use of structural templates (historically ‘ab initio’ modeling). Progress was driven by the successful application of deep learning techniques to predict inter-residue distances. In turn, these results drove dramatic improvements in three-dimensional structure accuracy: With the proviso that there are an adequate number of sequences known for the protein family, the new methods essentially solve the long-standing problem of predicting the fold topology of monomeric proteins. Further, the number of sequences required in the alignment has fallen substantially. There is also substantial improvement in the accuracy of template-based models. Other areas - model refinement, accuracy estimation, and the structure of protein assemblies - have again yielded interesting results. CASP13 placed increased emphasis on the use of sparse data together with modeling and chemical crosslinking, SAXS, and NMR all yielded more mature results. This paper summarizes the key outcomes of CASP13. The special issue of PROTEINS contains papers describing the CASP13 assessments in each modeling category and contributions from the participants

The Intrinsic Fundamental Group of a Linear Category

We provide an intrinsic definition of the fundamental group of a linear category over a ring as the automorphism group of the fibre functor on Galois coverings. If the universal covering exists, we prove that this group is isomorphic to the Galois group of the universal covering. The grading deduced from a Galois covering enables us to describe the canonical monomorphism from its automorphism group to the first Hochschild-Mitchell cohomology vector space.Comment: Final version, to appear in Algebras and Representation Theor

Rings of Frobenius operators

Let R be a local ring of prime characteristic. We study the ring of Frobenius operators F(E), where E is the injective hull of the residue field of R. In particular, we examine the finite generation of F(E) over its degree zero component, and show that F(E) need not be finitely generated when R is a determinantal ring; nonetheless, we obtain concrete descriptions of F(E) in good generality that we use, for example, to prove the discreteness of F-jumping numbers for arbitrary ideals in determinantal rings

The Waldschmidt constant for squarefree monomial ideals

Given a squarefree monomial ideal $I \subseteq R =k[x_1,\ldots,x_n]$, we show that $\widehat\alpha(I)$, the Waldschmidt constant of $I$, can be expressed as the optimal solution to a linear program constructed from the primary decomposition of $I$. By applying results from fractional graph theory, we can then express $\widehat\alpha(I)$ in terms of the fractional chromatic number of a hypergraph also constructed from the primary decomposition of $I$. Moreover, expressing $\widehat\alpha(I)$ as the solution to a linear program enables us to prove a Chudnovsky-like lower bound on $\widehat\alpha(I)$, thus verifying a conjecture of Cooper-Embree-H\`a-Hoefel for monomial ideals in the squarefree case. As an application, we compute the Waldschmidt constant and the resurgence for some families of squarefree monomial ideals. For example, we determine both constants for unions of general linear subspaces of $\mathbb{P}^n$ with few components compared to $n$, and we find the Waldschmidt constant for the Stanley-Reisner ideal of a uniform matroid.Comment: 26 pages. This project was started at the Mathematisches Forschungsinstitut Oberwolfach (MFO) as part of the mini-workshop "Ideals of Linear Subspaces, Their Symbolic Powers and Waring Problems" held in February 2015. Comments are welcome. Revised version corrects some typos, updates the references, and clarifies some hypotheses. To appear in the Journal of Algebraic Combinatoric

Tuning ultrafast electron thermalization pathways in a van der Waals heterostructure

Ultrafast electron thermalization - the process leading to Auger recombination, carrier multiplication via impact ionization and hot carrier luminescence - occurs when optically excited electrons in a material undergo rapid electron-electron scattering to redistribute excess energy and reach electronic thermal equilibrium. Due to extremely short time and length scales, the measurement and manipulation of electron thermalization in nanoscale devices remains challenging even with the most advanced ultrafast laser techniques. Here, we overcome this challenge by leveraging the atomic thinness of two-dimensional van der Waals (vdW) materials in order to introduce a highly tunable electron transfer pathway that directly competes with electron thermalization. We realize this scheme in a graphene-boron nitride-graphene (G-BN-G) vdW heterostructure, through which optically excited carriers are transported from one graphene layer to the other. By applying an interlayer bias voltage or varying the excitation photon energy, interlayer carrier transport can be controlled to occur faster or slower than the intralayer scattering events, thus effectively tuning the electron thermalization pathways in graphene. Our findings, which demonstrate a novel means to probe and directly modulate electron energy transport in nanoscale materials, represent an important step toward designing and implementing novel optoelectronic and energy-harvesting devices with tailored microscopic properties.Comment: Accepted to Nature Physic

An algorithm for producing F-pure ideals

This paper describes a method for computing all F-pure ideals for a given Cartier map of a polynomial ring over a finite field

Structure of the hDmc1-ssDNA filament reveals the principles of its architecture

In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination

Approaches in Sustainable, Biobased Multilayer Packaging Solutions

The depletion of fossil resources and the growing demand for plastic waste reduction has put industries and academic researchers under pressure to develop increasingly sustainable packaging solutions that are both functional and circularly designed. In this review, we provide an overview of the fundamentals and recent advances in biobased packaging materials, including new materials and techniques for their modification as well as their end-of-life scenarios. We also discuss the composition and modification of biobased films and multilayer structures, with particular attention to readily available drop-in solutions, as well as coating techniques. Moreover, we discuss end-of-life factors, including sorting systems, detection methods, composting options, and recycling and upcycling possibilities. Finally, regulatory aspects are pointed out for each application scenario and end-of-life option. Moreover, we discuss the human factor in terms of consumer perception and acceptance of upcycling

SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

<p>Abstract</p> <p>Background</p> <p>SHV β-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (<url>http://www.lahey.org/Studies/</url>). Besides, information about SHV β-lactamases can be found in the rapidly growing NCBI protein database. The SHV β-Lactamase Engineering Database (SHVED) has been developed to collect the SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions.</p> <p>Description</p> <p>The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.</p> <p>The SHVED is accessible at <url>http://www.LacED.uni-stuttgart.de/classA/SHVED/</url>. It provides sequences, structures, and a multisequence alignment of SHV β-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download.</p> <p>Conclusions</p> <p>The SHV β-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV β-lactamases.</p