Single-photon sampling architecture for solid-state imaging sensors
Ewout van den Berg, Emmanuel Candès, Garry Chinn, Craig Levin, Peter Demetri Olcott, and Carlos Sing-Long
We propose (pp. E2752–E2761) a highly compressed readout architecture for arrays of imaging sensors capable of detecting individual photons. By exploiting sparseness properties of the input signal, our architecture can provide the same information content as conventional readout designs while using orders of magnitude fewer output channels. This is achieved using a unique interconnection topology based on group-testing theoretical considerations. Unlike existing designs, this promises a low-cost sensor with high fill factor and high photon sensitivity, potentially enabling increased spatial and temporal resolution in a number of imaging applications, including positron-emission tomography and light detection and ranging.
Comparison of geomechanical deformation induced by megatonne-scale CO2 storage at Sleipner, Weyburn, and In Salah
James P. Verdon, J.-Michael Kendall, Anna L. Stork, R. Andy Chadwick, Don J. White, and Rob C. Bissell
The economic and political viability of carbon capture and sequestration (CCS) is dependent on the secure storage of CO2 in subsurface geologic reservoirs. A key leakage risk is that posed by geomechanical deformation generating fractures in otherwise sealing caprocks. This study (pp. E2762–E2771) examines this risk, comparing and contrasting deformation induced at three large-scale CCS sites—Sleipner (Norwegian North Sea), Weyburn (Canada), and In Salah (Algeria). These sites show very different geomechanical responses, highlighting the importance of systematic geomechanical appraisal prior to injection, and comprehensive, multifaceted monitoring during injection at any future large-scale CCS operations.
Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism
Melanie Gertz, Frank Fischer, Giang Thi Tuyet Nguyen, Mahadevan Lakshminarasimhan, Mike Schutkowski, Michael Weyand, and Clemens Steegborn
Sirtuin enzymes regulate metabolism and stress responses through deacetylation of specific protein lysine residues. Sirtuins are considered attractive drug targets, but selective inhibitors are rare, and their mechanisms mostly unknown. We report (pp. E2772–E2781) the mechanism of Sirtuin inhibition by Ex-527, a potent Sirt1 inhibitor widely used in physiological studies. A set of Sirtuin/ligand crystal structures, together with activity and binding data, reveals that the compound inhibits by forming a trimeric Sirtuin complex with a NAD+-derived coproduct. Our results yield insights in the unique Sirtuin catalytic mechanism and how it is exploited by Ex-527, and they provide essential information for rational drug development.
Thermodynamic origins of protein folding, allostery, and capsid formation in the human hepatitis B virus core protein
Crispin G. Alexander, Maike C. Jürgens, Dale A. Shepherd, Stefan M. V. Freund, Alison E. Ashcroft, and Neil Ferguson
Hepatitis B virus (HBV) is a major pathogen, yet no fully effective therapies exist. HBc is the multifunctional, capsid-forming protein essential for HBV replication. HBc structural plasticity is reportedly functionally important. We analyzed the folding mechanism of HBc using a multidisciplinary approach, including microscale thermophoresis and ion mobility spectrometry–mass spectrometry. HBc folds in a 3-state transition with a dimeric, helical intermediate. We found (E2782–E2791) evidence of a strained native ensemble wherein the energy landscapes for folding, allostery, and capsid formation are linked. Mutations thermodynamically trapped HBc in conformations unable to form capsids, suggesting chemical chaperones could elicit similar, potentially antiviral, effects.
Deciphering the rules by which 5′-UTR sequences affect protein expression in yeast
Shlomi Dvir, Lars Velten, Eilon Sharon, Danny Zeevi, Lucas B. Carey, Adina Weinberger, and Eran Segal
This study quantifies how protein levels are determined by the underlying 5′-UTR sequence of an mRNA. We accurately measured protein abundance in 2,041 5′-UTR sequence variants, differing only in positions −10 to −1. We show that a few nucleotide substitutions can significantly alter protein expression. We also developed a predictive model that explains two-thirds of the expression variation. We provide convincing evidence that key regulatory elements, including AUG sequence context, mRNA secondary structure, and out-of-frame upstream AUGs conjointly modulate protein levels. Our study (pp. E2792–E2801) can aid in synthetic biology applications, by suggesting sequence manipulations for fine-tuning protein expression in a predictable manner.
Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition
Antoine Cléry, Rahul Sinha, Olga Anczuków, Anna Corrionero, Ahmed Moursy, Gerrit M. Daubner, Juan Valcárcel, Adrian R. Krainer, and Frédéric H.-T. Allain
Serine/arginine (SR) proteins are key regulators of eukaryotic gene expression and have been associated with multiple human diseases including cancers. Several members of this protein family contain a noncanonical RNA recognition motif (RRM), the pseudo-RRM, for which the mode of RNA recognition is unknown. Here (pp. E2802–E2811), we solved the structure of SRSF1 pseudo-RRM bound to RNA. It reveals the RNA motif recognized and a very unusual mode of interaction, which is conserved for all the SR proteins containing pseudo-RRMs. Finally, we show that the pseudo-RRM in isolation often is sufficient to regulate splicing, and we reveal its mechanism of action.
Ultrahigh-resolution imaging reveals formation of neuronal SNARE/Munc18 complexes in situ
Alexandros Pertsinidis, Konark Mukherjee, Manu Sharma, Zhiping P. Pang, Sang Ryul Park, Yunxiang Zhang, Axel T. Brunger, Thomas C. Südhof, and Steven Chu
Synaptic vesicle fusion is catalyzed by multiprotein complexes that bring two lipid bilayers into close opposition. Several assembly mechanisms have been proposed for the synaptic vesicle fusion machinery, but exactly how these proteins interact in vivo remains unclear. We developed (pp. E2812–E2820) two-color fluorescence nanoscopy to directly visualize molecular interactions in situ and discovered that syntaxin-1, SNAP-25, and Munc18-1 (mammalian uncoordinated-18), three essential components for neurotransmission, closely colocalize on the plasma membrane, suggesting possible pathways for SNARE-mediated membrane fusion. Our superresolution method provides a framework for delineating the molecular underpinnings of the synaptic vesicle fusion machinery.
Evolutionary diversification of the multimeric states of proteins
Michael Lynch
Rather than operating as single units, most proteins assemble as multimers, usually with all subunits derived from the same gene. In contrast to patterns of gene structure and genome organization, which typically exhibit substantial increases in complexity from unicellular to multicellular organisms, the structural complexity of orthologous proteins appears roughly constant over the tree of life. The interfaces of multimers also often shift dramatically over evolutionary time. To explain these observations (pp. E2821–E2828), a model is presented for the stochastic origin of variation in the multimeric states of proteins via the joint processes of mutation, random genetic drift, and constant directional selection.
Structural insights into the regulation of sialic acid catabolism by the Vibrio vulnificus transcriptional repressor NanR
Jungwon Hwang, Byoung Sik Kim, Song Yee Jang, Jong Gyu Lim, Dong-Ju You, Hyun Suk Jung, Tae-Kwang Oh, Jie-Oh Lee, Sang Ho Choi, and Myung Hee Kim
Pathogenic bacteria that experience limited nutrient availability in the host gut have evolved sophisticated systems to catabolize N-acetylneuraminic acid (Neu5Ac; sialic acid). This study (pp. E2829–E2837) reports the structural analysis of NanR, a repressor of the N-acetylneuraminate (nan) genes responsible for Neu5Ac catabolism, complexed with its regulatory ligand, N-acetylmannosamine 6-phosphate (ManNAc-6P). The interaction between NanR and the nan promoter is alleviated by the ManNAc-6P–mediated relocation of residues in the ligand-binding domain of NanR, which subsequently relieves the repressive effect of NanR and induces the transcription of nan genes. These events are required for survival and for Vibrio vulnificus pathogenesis.
Torins are potent antimalarials that block replenishment of Plasmodium liver stage parasitophorous vacuole membrane proteins
Kirsten K. Hanson, Ana S. Ressurreição, Kathrin Buchholz, Miguel Prudêncio, Jonathan D. Herman-Ornelas, Maria Rebelo, Wandy L. Beatty, Dyann F. Wirth, Thomas Hänscheid, Rui Moreira, Matthias Marti, and Maria M. Mota
Plasmodium parasites have two distinct intracellular growth stages inside the mammalian host—the first stage, which is clinically silent, in liver hepatocytes, and the second, which causes the symptoms of malaria, in red blood cells. This study reports the discovery of a class of antimalarial compounds called torins, which are extremely potent inhibitors of both intracellular stages of Plasmodium. We show (pp. E2838–E2847) that torins block trafficking of liver stage parasite proteins to the physical host–parasite interface, called the parasitophorous vacuole membrane (PVM), and that without continuous trafficking of PVM-resident proteins, the parasite is subject to elimination by its host hepatocyte.
Geminin deploys multiple mechanisms to regulate Cdt1 before cell division thus ensuring the proper execution of DNA replication
Andrea Ballabeni, Raffaella Zamponi, Jodene K. Moore, Kristian Helin, and Marc W. Kirschner
The master cell-cycle processes governing DNA replication and mitosis in eukaryotic cells are regulated by cyclin/cyclin dependent kinase 1 and the anaphase-promoting complex, with checkpoint activity on these regulators. It is not these regulators but rather intermediaries that communicate to the processes. Here we show that the protein Geminin acts centrally in controlling DNA replication by ensuring that DNA is replicated during S phase and only once. This paper (pp. E2848–E2853) describes the Geminin “sub-master” regulatory circuit and the central role of Geminin in controlling events of the cell cycle.