TY - JOUR AB - Populations of neurons in motor cortex engage in complex transient dynamics of large amplitude during the execution of limb movements. Traditional network models with stochastically assigned synapses cannot reproduce this behavior. Here we introduce a class of cortical architectures with strong and random excitatory recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from a control theory perspective. Such networks transiently amplify specific activity states and can be used to reliably execute multidimensional movement patterns. Similar to the experimental observations, these transients must be preceded by a steady-state initialization phase from which the network relaxes back into the background state by way of complex internal dynamics. In our networks, excitation and inhibition are as tightly balanced as recently reported in experiments across several brain areas, suggesting inhibitory control of complex excitatory recurrence as a generic organizational principle in cortex. AU - Hennequin, Guillaume AU - Vogels, Tim P AU - Gerstner, Wulfram ID - 8022 IS - 6 JF - Neuron SN - 0896-6273 TI - Optimal control of transient dynamics in balanced networks supports generation of complex movements VL - 82 ER - TY - JOUR AB - The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position. AU - Bharata, Tanmay A AU - Menendez, Luis R AU - Hagena, Wim J AU - Luxd, Vanda AU - Igonete, Sebastien AU - Schorba, Martin AU - Florian Schur AU - Kraüsslich, Hans Georg AU - Briggsa, John A ID - 809 IS - 22 JF - PNAS TI - Cryo electron microscopy of tubular arrays of HIV-1 Gag resolves structures essential for immature virus assembly VL - 111 ER - TY - JOUR AB - Passive immunotherapy with monoclonal antibodies represents a cornerstone of human anticancer therapies, but has not been established in veterinary medicine yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab in human clinical oncology, we present here a “caninized” version of this antibody, can225IgG, for comparative oncology studies. Variable region genes of 225, the murine precursor of cetuximab, were fused with canine constant heavy gamma and kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO) DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected according to productivity and highest specificity in EGFR-coated ELISA. Upon purification with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity, correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing cells was assessed by flow cytometry and immunofluorescence; moreover, binding to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability and proliferation assays, incubation with can225IgG led to significant tumor cell growth inhibition. Moreover, this antibody mediated significant tumor cell killing via phagocytosis in vitro. We thus present here, for the first time, the generation of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like binding site, on the one hand, and the expression of a 91% homologous EGFR molecule in canine cancer, on the other hand, this antibody may be a promising research compound to establish passive immunotherapy in dog patients with cancer. AU - Singer, J. AU - Fazekas, Judit AU - Wang, W. AU - Weichselbaumer, M. AU - Matz, M. AU - Mader, A. AU - Steinfellner, W. AU - Meitz, S. AU - Mechtcheriakova, D. AU - Sobanov, Y. AU - Willmann, M. AU - Stockner, T. AU - Spillner, E. AU - Kunert, R. AU - Jensen-Jarolim, E. ID - 8244 IS - 7 JF - Molecular Cancer Therapeutics SN - 1535-7163 TI - Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy in dog cancer patients VL - 13 ER - TY - JOUR AB - Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion of biomolecules at the atomic level. One technique, the analysis of relaxation dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics of biological processes. Built on top of the relax computational environment for NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate and easy-to-use. The software supports more models, both numeric and analytic, than current solutions. An automated protocol, available for scripting and driving the graphical user interface (GUI), is designed to simplify the analysis of dispersion data for NMR spectroscopists. Decreases in optimization time are granted by parallelization for running on computer clusters and by skipping an initial grid search by using parameters from one solution as the starting point for another —using analytic model results for the numeric models, taking advantage of model nesting, and using averaged non-clustered results for the clustered analysis. AU - Morin, Sébastien AU - Linnet, Troels E AU - Lescanne, Mathilde AU - Schanda, Paul AU - Thompson, Gary S AU - Tollinger, Martin AU - Teilum, Kaare AU - Gagné, Stéphane AU - Marion, Dominique AU - Griesinger, Christian AU - Blackledge, Martin AU - d’Auvergne, Edward J ID - 8459 IS - 15 JF - Bioinformatics KW - Statistics and Probability KW - Computational Theory and Mathematics KW - Biochemistry KW - Molecular Biology KW - Computational Mathematics KW - Computer Science Applications SN - 1367-4803 TI - Relax: The analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data VL - 30 ER - TY - JOUR AB - The maintenance of bacterial cell shape and integrity is largely attributed to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform this cross-linking are important targets for antibiotics. Despite this biomedical importance, to date no structure of a protein in complex with an intact bacterial peptidoglycan has been resolved, primarily due to the large size and flexibility of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly, the model obtained from protein chemical shift perturbation data shows that both domains—the catalytic domain as well as the proposed peptidoglycan recognition domain—are important for the interaction and reveals a novel binding motif that involves residues outside of the classical enzymatic pocket. Experiments on mutants and truncated protein constructs independently confirm the binding site and the implication of both domains. Through measurements of dipolar-coupling derived order parameters of bond motion we show that protein binding reduces the flexibility of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases. The strategy developed here can be extended to the study of a large variety of enzymes involved in peptidoglycan morphogenesis. AU - Schanda, Paul AU - Triboulet, Sébastien AU - Laguri, Cédric AU - Bougault, Catherine M. AU - Ayala, Isabel AU - Callon, Morgane AU - Arthur, Michel AU - Simorre, Jean-Pierre ID - 8458 IS - 51 JF - Journal of the American Chemical Society SN - 0002-7863 TI - Atomic model of a cell-wall cross-linking enzyme in complex with an intact bacterial peptidoglycan VL - 136 ER - TY - JOUR AB - The function of proteins depends on their ability to sample a variety of states differing in structure and free energy. Deciphering how the various thermally accessible conformations are connected, and understanding their structures and relative energies is crucial in rationalizing protein function. Many biomolecular reactions take place within microseconds to milliseconds, and this timescale is therefore of central functional importance. Here we show that R1ρ relaxation dispersion experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible to investigate the thermodynamics and kinetics of such exchange process, and gain insight into structural features of short‐lived states. AU - Ma, Peixiang AU - Haller, Jens D. AU - Zajakala, Jérémy AU - Macek, Pavel AU - Sivertsen, Astrid C. AU - Willbold, Dieter AU - Boisbouvier, Jérôme AU - Schanda, Paul ID - 8460 IS - 17 JF - Angewandte Chemie International Edition SN - 1433-7851 TI - Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy VL - 53 ER - TY - JOUR AB - In this paper, we study small perturbations of a class of non-convex integrable Hamiltonians with two degrees of freedom, and we prove a result of diffusion for an open and dense set of perturbations, with an optimal time of diffusion which grows linearly with respect to the inverse of the size of the perturbation. AU - Bounemoura, Abed AU - Kaloshin, Vadim ID - 8501 IS - 2 JF - Moscow Mathematical Journal KW - General Mathematics SN - 1609-3321 TI - Generic fast diffusion for a class of non-convex Hamiltonians with two degrees of freedom VL - 14 ER - TY - JOUR AB - The main model studied in this paper is a lattice of pendula with a nearest‐neighbor coupling. If the coupling is weak, then the system is near‐integrable and KAM tori fill most of the phase space. For all KAM trajectories the energy of each pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily weak coupling of a certain localized type, the neighboring pendula can exchange energy. In fact, the energy can be transferred between the pendula in any prescribed way. AU - Kaloshin, Vadim AU - Levi, Mark AU - Saprykina, Maria ID - 8500 IS - 5 JF - Communications on Pure and Applied Mathematics KW - Applied Mathematics KW - General Mathematics SN - 0010-3640 TI - Arnol′d diffusion in a pendulum lattice VL - 67 ER - TY - JOUR AB - Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on howlong the gene copies continue to experience an elevated rate of evolution remain scarce. Standard theory of gene duplications based on some level of genetic redundancy of gene copies predicts that the period of accelerated evolutionmust end relatively quickly. Using a maximum-likelihood approach we estimate preduplication, initial postduplication, and recent postduplication rates of evolution that occurred in themammalian lineage.Wefind that both gene copies experience a similar in magnitude acceleration in their rate of evolution. The copy located in the original genomic position typically returns to the preduplication rates of evolution in a short period of time. The burst of faster evolution of the copy that is located in a new genomic position typically lasts longer. Furthermore, the fast-evolving copies on average continue to evolve faster than the preduplication rates far longer than predicted by standard theory of gene duplications.We hypothesize that the prolonged elevated rates of evolution are determined by functional properties that were acquired during, or soon after, the gene duplication event. AU - Rosello, Oriol P AU - Fyodor Kondrashov ID - 852 IS - 8 JF - Genome Biology and Evolution TI - Long-Term asymmetrical acceleration of protein evolution after gene duplication VL - 6 ER - TY - JOUR AB - The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paralogue evolved increased binding specificity so that it only binds one type of motif, whereas the other copy evolved a decreased activity so that it only activates promoters that contain multiple binding sites. Interestingly, only a few mutations in both the DNA-binding domains and in the promoter binding sites were required to gradually disentangle the two networks. These results reveal how duplication of a promiscuous transcription factor followed by concerted cis and trans mutations allows expansion of a regulatory network. AU - Pougach, Ksenia S AU - Voet, Arnout R AU - Fyodor Kondrashov AU - Voordeckers, Karin AU - Christiaens, Joaquin F AU - Baying, Bianka AU - Bénès, Vladimı́r AU - Sakai, Ryo AU - Aerts, Jan A AU - Zhu, Bo AU - Van Dijck, Patrick AU - Verstrepen, Kevin J ID - 856 JF - Nature Communications TI - Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network VL - 5 ER -