Polymeric Impulsive Actuation Mechanisms: Development, Characterization, and Modeling
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Structural Insight Into Marburg Virus Nucleoprotein-RNA Complex Formation
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.13.452116; this version posted July 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Structural insight into Marburg virus nucleoprotein-RNA complex formation 2 3 Yoko Fujita-Fujiharu1,2,3, Yukihiko Sugita1,2,4, Yuki Takamatsu1,#, Kazuya Houri1,2,3, Manabu 4 Igarashi5, Yukiko Muramoto1,2,3, Masahiro Nakano1,2,3, Yugo Tsunoda1, Stephan Becker6,7, 5 Takeshi Noda1,2,3* 6 7 1 Laboratory of Ultrastructural Virology, Institute for Frontier Life and Medical Sciences, 8 Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan 9 2 Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 10 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan 11 3 CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332- 12 0012, Japan 13 4 Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan. 14 5 Division of Epidemiology, International Institute for Zoonosis Control, Hokkaido University, 15 Sapporo 001-0020, Japan 16 6 Institute of Virology, University of Marburg, 35043 Marburg, Germany. 17 7 German Center for Infection Research (DZIF), Marburg-Gießen-Langen Site, University of 18 Marburg, 35043 Marburg, Germany. 19 20 # present address: Department of Virology I, National Institute of Infectious Diseases, Gakuen 21 4-7-1, Musashimurayama-city, Tokyo 208-0011, Japan 22 *correspondence to: [email protected] 23 24 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.13.452116; this version posted July 13, 2021. -
Α/Β Coiled Coils 2 3 Marcus D
1 α/β Coiled Coils 2 3 Marcus D. Hartmann, Claudia T. Mendler†, Jens Bassler, Ioanna Karamichali, Oswin 4 Ridderbusch‡, Andrei N. Lupas* and Birte Hernandez Alvarez* 5 6 Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 7 Tübingen, Germany 8 † present address: Nuklearmedizinische Klinik und Poliklinik, Klinikum rechts der Isar, 9 Technische Universität München, Munich, Germany 10 ‡ present address: Vossius & Partner, Siebertstraße 3, 81675 Munich, Germany 11 12 13 14 * correspondence to A. N. Lupas or B. Hernandez Alvarez: 15 Department of Protein Evolution 16 Max-Planck-Institute for Developmental Biology 17 Spemannstr. 35 18 D-72076 Tübingen 19 Germany 20 Tel. –49 7071 601 356 21 Fax –49 7071 601 349 22 [email protected], [email protected] 23 1 24 Abstract 25 Coiled coils are the best-understood protein fold, as their backbone structure can uniquely be 26 described by parametric equations. This level of understanding has allowed their manipulation 27 in unprecedented detail. They do not seem a likely source of surprises, yet we describe here 28 the unexpected formation of a new type of fiber by the simple insertion of two or six residues 29 into the underlying heptad repeat of a parallel, trimeric coiled coil. These insertions strain the 30 supercoil to the breaking point, causing the local formation of short β-strands, which move the 31 path of the chain by 120° around the trimer axis. The result is an α/β coiled coil, which retains 32 only one backbone hydrogen bond per repeat unit from the parent coiled coil. -
Limits of Pgl(3)-Translates of Plane Curves, I
LIMITS OF PGL(3)-TRANSLATES OF PLANE CURVES, I PAOLO ALUFFI, CAREL FABER Abstract. We classify all possible limits of families of translates of a fixed, arbitrary complex plane curve. We do this by giving a set-theoretic description of the projective normal cone (PNC) of the base scheme of a natural rational map, determined by the curve, 8 N from the P of 3 × 3 matrices to the P of plane curves of degree d. In a sequel to this paper we determine the multiplicities of the components of the PNC. The knowledge of the PNC as a cycle is essential in our computation of the degree of the PGL(3)-orbit closure of an arbitrary plane curve, performed in [5]. 1. Introduction In this paper we determine the possible limits of a fixed, arbitrary complex plane curve C , obtained by applying to it a family of translations α(t) centered at a singular transformation of the plane. In other words, we describe the curves in the boundary of the PGL(3)-orbit closure of a given curve C . Our main motivation for this work comes from enumerative geometry. In [5] we have determined the degree of the PGL(3)-orbit closure of an arbitrary (possibly singular, re- ducible, non-reduced) plane curve; this includes as special cases the determination of several characteristic numbers of families of plane curves, the degrees of certain maps to moduli spaces of plane curves, and isotrivial versions of the Gromov-Witten invariants of the plane. A description of the limits of a curve, and in fact a more refined type of information is an essential ingredient of our approach. -
Stapled Peptides—A Useful Improvement for Peptide-Based Drugs
molecules Review Stapled Peptides—A Useful Improvement for Peptide-Based Drugs Mattia Moiola, Misal G. Memeo and Paolo Quadrelli * Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; [email protected] (M.M.); [email protected] (M.G.M.) * Correspondence: [email protected]; Tel.: +39-0382-987315 Received: 30 July 2019; Accepted: 1 October 2019; Published: 10 October 2019 Abstract: Peptide-based drugs, despite being relegated as niche pharmaceuticals for years, are now capturing more and more attention from the scientific community. The main problem for these kinds of pharmacological compounds was the low degree of cellular uptake, which relegates the application of peptide-drugs to extracellular targets. In recent years, many new techniques have been developed in order to bypass the intrinsic problem of this kind of pharmaceuticals. One of these features is the use of stapled peptides. Stapled peptides consist of peptide chains that bring an external brace that force the peptide structure into an a-helical one. The cross-link is obtained by the linkage of the side chains of opportune-modified amino acids posed at the right distance inside the peptide chain. In this account, we report the main stapling methodologies currently employed or under development and the synthetic pathways involved in the amino acid modifications. Moreover, we report the results of two comparative studies upon different kinds of stapled-peptides, evaluating the properties given from each typology of staple to the target peptide and discussing the best choices for the use of this feature in peptide-drug synthesis. Keywords: stapled peptide; structurally constrained peptide; cellular uptake; helicity; peptide drugs 1. -
Unsupervised Smooth Contour Detection
Published in Image Processing On Line on 2016–11–18. Submitted on 2016–04–21, accepted on 2016–10–03. ISSN 2105–1232 c 2016 IPOL & the authors CC–BY–NC–SA This article is available online with supplementary materials, software, datasets and online demo at https://doi.org/10.5201/ipol.2016.175 2015/06/16 v0.5.1 IPOL article class Unsupervised Smooth Contour Detection Rafael Grompone von Gioi1, Gregory Randall2 1 CMLA, ENS Cachan, France ([email protected]) 2 IIE, Universidad de la Rep´ublica, Uruguay ([email protected]) Abstract An unsupervised method for detecting smooth contours in digital images is proposed. Following the a contrario approach, the starting point is defining the conditions where contours should not be detected: soft gradient regions contaminated by noise. To achieve this, low frequencies are removed from the input image. Then, contours are validated as the frontiers separating two adjacent regions, one with significantly larger values than the other. Significance is evalu- ated using the Mann-Whitney U test to determine whether the samples were drawn from the same distribution or not. This test makes no assumption on the distributions. The resulting algorithm is similar to the classic Marr-Hildreth edge detector, with the addition of the statis- tical validation step. Combined with heuristics based on the Canny and Devernay methods, an efficient algorithm is derived producing sub-pixel contours. Source Code The ANSI C source code for this algorithm, which is part of this publication, and an online demo are available from the web page of this article1. -
The Generic Geometry of Helices and Their Close-Packed Structures
Theor Chem Acc (2010) 125:207–215 DOI 10.1007/s00214-009-0639-4 REGULAR ARTICLE The generic geometry of helices and their close-packed structures Kasper Olsen Æ Jakob Bohr Received: 23 May 2009 / Accepted: 9 September 2009 / Published online: 25 September 2009 Ó The Author(s) 2009. This article is published with open access at Springerlink.com Abstract The formation of helices is an ubiquitous 1 Introduction phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical struc- Helical structures are common in chain molecules such as tures have geometrical constraints analogous to close- proteins, RNA, and DNA, e.g., a-helices and the A, B and Z packing of three-dimensional crystal structures. For helical forms of DNA. In this paper, we consider the packing of packing the geometrical constraints involve parameters idealized helices formed by a continuous tube with the such as the radius of the helical cylinder, the helical pitch purpose to calculate the constraints on such helices which angle, and the helical tube radius. In this communication, arise from close-packing and space filling considerations; the geometrical constraints for single helix, double helix, we consider single helical tubes, as well as sets of two and for double helices with minor and major grooves are identical helical tubes. It is found that the efficiency of the calculated. The results are compared with values from the use of space depends on the helical pitch angle, and the literature for helical polypeptide backbone structures, the optimum helical pitch angle is determined for single and a-, p-, 310-, and c-helices. -
Breaking Non-Native Hydrophobic Clusters Is the Rate-Limiting Step In
Shibasish Chowdhury Wei Zhang Breaking Non-Native Chun Wu Guoming Xiong Hydrophobic Clusters is the Yong Duan Rate-Limiting Step in the Department of Chemistry and Biochemistry, Folding of an Alanine-Based Center of Biomedical Research Excellence, Peptide University of Delaware, Newark, DE 19716 Received 13 March 2002; accepted 29 April 2002 Abstract: The formation mechanism of an alanine-based peptide has been studied by all-atom molecular dynamics simulations with a recently developed all-atom point-charge force field and the Generalize Born continuum solvent model at an effective salt concentration of 0.2M. Thirty-two simulations were conducted. Each simulation was performed for 100 ns. A surprisingly complex folding process was observed. The development of the helical content can be divided into three phases with time constants of 0.06–0.08, 1.4–2.3, and 12–13 ns, respectively. Helices initiate extreme rapidly in the first phase similar to that estimated from explicit solvent simulations. Hydrophobic collapse also takes place in this phase. A folding intermediate state develops in the second phase and is unfolded to allow the peptide to reach the transition state in the third phase. The folding intermediate states are characterized by the two-turn short helices and the transition states are helix–turn–helix motifs—both of which are stabilized by hydrophobic clusters. The equilibrium helical content, calculated by both the main-chain ⌽–⌿ torsion angles and the main-chain hydrogen bonds, is 64–66%, which is in remarkable agreement with experiments. After corrected for the solvent viscosity effect, an extrapolated folding time of 16–20 ns is obtained that is in qualitative agreement with experiments. -
Calculus-Free Derivatives of Sine and Cosine
Calculus-free Derivatives of Sine and Cosine B.D.S. McConnell [email protected] Wrap a square smoothly around a cylinder, and the curved images of the square’s diagonals will trace out helices, with the (original, uncurved) diag- onals tangent to those curves. Projecting these elements into appropriate planes reveals an intuitive, geometric development of the formulas for the derivatives of sine and cosine, with no quotient of vanishing differences re- quired. Indeed, a single —almost-“Behold!”-worthy— diagram and a short notational summary (see the last page of this note) give everything away. The setup. Consider a cylinder (“C”) of radius 1 and a unit square (“S”), with a pair of S’s edges parallel to C’s axis, and with S’s center (“P ”) a point of tangency with C’s surface. We may assume that the cylinder’s axis coincides with the z axis; we may also assume that, measuring along the surface of the cylinder, the (straight-line) distance from P to the xy-plane is equal to the (arc-of-circle) distance from P to the zx-plane. That is, we take P to have coordinates (cos θ0, sin θ0, θ0) for some θ0, where cos() and sin() take radian arguments. Wrapping S around C causes the image of an extended diagonal of S to trace out the helix (“H”) containing all (and only) points of the form (cos θ, sin θ, θ). Moreover, the original, uncurved diagonal segment of S de- termines a vector, v :=< vx, vy, vz >, tangent to H at P ; taking vz = 1, we assure that the vector conveniently points “forward” (that is, in the direction of increasing θ) along the helix. -
Structure of Voltage-Modulated Sodium-Selective NALCN-FAM155A Channel Complex ✉ Yunlu Kang 1, Jing-Xiang Wu1,2,3 & Lei Chen 1,2,3
ARTICLE https://doi.org/10.1038/s41467-020-20002-9 OPEN Structure of voltage-modulated sodium-selective NALCN-FAM155A channel complex ✉ Yunlu Kang 1, Jing-Xiang Wu1,2,3 & Lei Chen 1,2,3 Resting membrane potential determines the excitability of the cell and is essential for the cellular electrical activities. The NALCN channel mediates sodium leak currents, which positively adjust resting membrane potential towards depolarization. The NALCN channel is 1234567890():,; involved in several neurological processes and has been implicated in a spectrum of neu- rodevelopmental diseases. Here, we report the cryo-EM structure of rat NALCN and mouse FAM155A complex to 2.7 Å resolution. The structure reveals detailed interactions between NALCN and the extracellular cysteine-rich domain of FAM155A. We find that the non- canonical architecture of NALCN selectivity filter dictates its sodium selectivity and calcium block, and that the asymmetric arrangement of two functional voltage sensors confers the modulation by membrane potential. Moreover, mutations associated with human diseases map to the domain-domain interfaces or the pore domain of NALCN, intuitively suggesting their pathological mechanisms. 1 State Key Laboratory of Membrane Biology, College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, 100871 Beijing, China. 2 Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China. ✉ 3 Academy for Advanced Interdisciplinary Studies, Peking University, 100871 Beijing, China. email: [email protected] NATURE COMMUNICATIONS | (2020) 11:6199 | https://doi.org/10.1038/s41467-020-20002-9 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-020-20002-9 ALCN channel is a voltage-modulated sodium-selective Therefore, we started with the cryo-EM studies of the NALCN– ion channel1. -
Geometry of Algebraic Curves
Geometry of Algebraic Curves Lectures delivered by Joe Harris Notes by Akhil Mathew Fall 2011, Harvard Contents Lecture 1 9/2 x1 Introduction 5 x2 Topics 5 x3 Basics 6 x4 Homework 11 Lecture 2 9/7 x1 Riemann surfaces associated to a polynomial 11 x2 IOUs from last time: the degree of KX , the Riemann-Hurwitz relation 13 x3 Maps to projective space 15 x4 Trefoils 16 Lecture 3 9/9 x1 The criterion for very ampleness 17 x2 Hyperelliptic curves 18 x3 Properties of projective varieties 19 x4 The adjunction formula 20 x5 Starting the course proper 21 Lecture 4 9/12 x1 Motivation 23 x2 A really horrible answer 24 x3 Plane curves birational to a given curve 25 x4 Statement of the result 26 Lecture 5 9/16 x1 Homework 27 x2 Abel's theorem 27 x3 Consequences of Abel's theorem 29 x4 Curves of genus one 31 x5 Genus two, beginnings 32 Lecture 6 9/21 x1 Differentials on smooth plane curves 34 x2 The more general problem 36 x3 Differentials on general curves 37 x4 Finding L(D) on a general curve 39 Lecture 7 9/23 x1 More on L(D) 40 x2 Riemann-Roch 41 x3 Sheaf cohomology 43 Lecture 8 9/28 x1 Divisors for g = 3; hyperelliptic curves 46 x2 g = 4 48 x3 g = 5 50 1 Lecture 9 9/30 x1 Low genus examples 51 x2 The Hurwitz bound 52 2.1 Step 1 . 53 2.2 Step 10 ................................. 54 2.3 Step 100 ................................ 54 2.4 Step 2 . -
Structural and Biochemical Insights Into the Multiple Functions of Yeast Grx3
Article Structural and Biochemical Insights into the Multiple Functions of Yeast Grx3 Chang-Biao Chi, YaJun Tang, Jiahai Zhang, Ya-Nan Dai, Mohnad Abdalla, Yuxing Chen and Cong-Zhao Zhou School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China Key Laboratory of Structural Biology, Chinese Academy of Science, Hefei, Anhui, 230027, People's Republic of China Correspondence to YaJun Tang and Cong-Zhao Zhou: School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China. [email protected]; [email protected] https://doi.org/10.1016/j.jmb.2018.02.024 Edited by Charalampo Kalodimos Abstract The yeast Saccharomyces cerevisiae monothiol glutaredoxin Grx3 plays a key role in cellular defense against oxidative stress and more importantly, cooperates with BolA-like iron repressor of activation protein Fra2 to regulate the localization of the iron-sensing transcription factor Aft2. The interplay among Grx3, Fra2 and Aft2 responsible for the regulation of iron homeostasis has not been clearly described. Here we solved the crystal structures of the Trx domain (Grx3Trx) and Grx domain (Grx3Grx) of Grx3 in addition to the solution structure of Fra2. Structural analyses and activity assays indicated that the Trx domain also contributes to the glutathione S-transferase activity of Grx3, via an inter-domain disulfide bond between Cys37 and Cys176. NMR titration and pull-down assays combined with surface plasmon resonance experiments revealed that Fra2 could form a noncovalent heterodimer with Grx3 via an interface between the helix-turn-helix motif of Fra2 and the C- terminal segment of Grx3Grx, different from the previously identified covalent heterodimer mediated by Fe–S cluster. -
Perylene Diimide: a Versatile Building Block for Complex Molecular Architectures and a Stable Charge Storage Material
Perylene Diimide: A Versatile Building Block for Complex Molecular Architectures and a Stable Charge Storage Material Margarita Milton Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2018 © 2018 Margarita Milton All rights reserved ABSTRACT Perylene Diimide: A Versatile Building Block for Complex Molecular Architectures and a Stable Charge Storage Material Margarita Milton Properties such as chemical robustness, potential for synthetic tunability, and superior electron-accepting character describe the chromophore perylene-3,4,9,10-tetracarboxylic diimide (PDI) and have enabled its penetration into organic photovoltaics. The ability to extend what is already a large aromatic core allows for synthesis of graphene ribbon PDI oligomers. Functionalization with polar and ionic groups leads to liquid crystalline phases or immense supramolecular architectures. Significantly, PDI dianions can survive in water for two months with no decomposition, an important property for charge storage materials. We realized the potential of PDI as an efficient negative-side material for Redox Flow Batteries (RFBs). The synthetic tunability of PDI allowed for screening of several derivatives with side chains that enhanced solubility in polar solvents. The optimized molecule, PDI[TFSI]2, dissolved in acetonitrile up to 0.5 M. For the positive-side, we synthesized the ferrocene oil [Fc4] in high yield. The large hydrodynamic radii of PDI[TFSI]2 and [Fc4] preclude their ability to cross a size exclusion membrane, which is a cheap alternative to the typical RFB membranes. We show that this cellulose-based membrane can support high voltages in excess of 3 V and extreme temperatures (−20 to 110 °C).