ADVANCES IN STRUCTURAL BIOLOGY

MiniSimpozij 2017

ADVANCES IN STRUCTURAL BIOLOGY

26

October 2017 Ljubljana

Department of Molecular Biology and Nanobiotechnology D11

National Institute of Chemistry

MiniSimpozij 2017

ADVANCES IN STRUCTURAL

BIOLOGY

CIP - Kataložni zapis o publikaciji

Narodna in univerzitetna knjižnica, Ljubljana 577.2(082)

ADVANCES in structural biology : mini simpozij 2017, [26th October 2017

Ljubljana] / [editors Gregor Anderluh & Marjetka Podobnik]. - Ljubljana : Department of Molecular Biology and Nanobiotechnology D11, National Institute of Chemistry, 2017 ISBN 978-961-6104-37-1

1. Anderluh, Gregor, 1969- 292397056

6^th MiniSimpozij 2017

ADVANCES IN STRUCTURAL BIOLOGY Organised by

Katja Pirc, Simon Žurga & Marjetka Podobnik

Department of Molecular Biology and Nanobiotechnology D11 National Institute of Chemistry

Editors

Gregor Anderluh & Marjetka Podobnik Technical editors

Matic Kisovec, Katja Pirc & Simon Žurga Issued by

Department of Molecular Biology and Nanobiotechnology D11 National Institute of Chemistry

Printed by Infokart

Ljubljana, 2017

Contents

Program 4

Foreword 5

Department of Molecular Biology and Nanobiotechnology 6

Abstract of the plenary lecture 8

Abstracts of short lectures 10

4

Program

14.00-14.20 Marjetka Podobnik

& Gregor Anderluh

Welcome speech

14.20-14.50 Jiří Nováček Structure and genome delivery mechanism of Staphylococcus aureus phage therapy agent phi812-K1 determined by cryo- electron microscopy

14.50-15.10 Andreja Šink Structural studies of flexible filamentous virus

15.10-15.30 Nada Žnidaršič Conventional transmission electron microscopy as a complementary tool in imaging of macromolecules and macromolecular assemblies 15.30-15.50 Magda Tušek

Žnidarič Negative staining method for transmission electron microscopy of biological samples – the player in the team

15.50-16.10 Elena Tchernychova Advanced transmission electron microscopy at NIC

16.10-16.30 Samo Hudoklin Electron tomography of cellular structures 16.30-16.50 Damijan Knez Structure-based drug design: from selective

butyrylcholinesterase inhibitors towards multifunctional anti-Alzheimer ligands 16.50-17.10 Dušan Turk Rfree: a dinosaur marked for extinction?

17.10-17.40 Coffee break

17.40-18.00 Silvia Onesti Macromolecular machines involved in DNA replication: an integrated structural biology approach

18.00-18.20 Miha Pavšič Tail and intermodule linker flexibility of testicans explored by SAXS

18.20-18.40 Ajasja Ljubetič Coiled-coil protein origami cages (capable of in vivo self-assembly)

18.40-19.00 JEOL-SCAN Corporate presentation 19.00-19.20 Thermo Fischer

Scientific

Corporate presentation 19.20-19.25 Marjetka Podobnik Closing remarks

5

Foreword

Welcome,

to the traditional 6^th MiniSimpozij organized by Department of Molecular Biology and Nanobiotechnology. We study molecular background of various biological processes at different resolution levels, and in particular focus on interactions between biological molecules and their mechanism of action. In addition, we attempt to translate the potential of these molecules into various biotechnological applications.

The main goal of these mini-symposia is to get together a local scientific community as well as colleagues from abroad to share our scientific knowledge, expertise and experience, and to continue (or hopefully start new) collaborations, or to simply educate us in various research topics and methodological approaches.

The title of this year’s mini-symposium is “ADVANCES IN STRUCTURAL BIOLOGY”.

Therefore, our program includes presentations by invited speakers who use different approaches of biophysics and structural biology to elucidate structural properties of various biological systems as well as those provided by synthetic biology, at different resolution levels. Importantly, in the light of recent extraordinary advances is the field as well as the Nobel Prize Award for Chemistry for 2017, we are paying a special attention to different modes of electron microscopy, in particular cryo-electron microscopy. We strongly believe that many Slovenian scientists are highly interested in this powerful methodological approach and should have an opportunity to become educated in the usage of this technique, and moreover, to actually have the state-of- the-art equipment, which Slovenian scientists are lacking at the time being.

This year we have eleven invited speakers, including guests from aboard. In addition, the representatives of two companies producing high-end (cryo)-electron microscopes will give their presentations and have stands in front of the lecture room. The official language of the meeting is English.

We wish you all a pleasant and fruitful meeting, with lively scientific discussions between presentations, during the coffee break and after the meeting. Let us hope that the meeting will bring along new collaborations and a positive outlook for the Slovenian science, especially in the field of cryo-electron microscopy.

Assist. Prof. Marjetka Podobnik Prof. Gregor Anderluh

6

Department of Molecular Biology and Nanobiotechnology D11

We are performing top level research of biological processes, focusing on understanding the mechanism of action of proteins and molecular interactions. We create new basic knowledge as well as introduce modern methodologies in the field of Life Sciences. We develop applications for solving actual problems in biotechnology and pharmaceutical industry, in particular in development of biological drugs. Head of department is Assist. Prof. Marjetka Podobnik, PhD.

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Past events organised by

Department of Molecular Biology and Nanobiotechnology D11

MiniSimpozij 2012

PLANT-PATHOGEN INTERACTIONS National Institute of Chemistry, Ljubljana, 16.2.2012 https://www.ki.si/odseki/d11-odsek-za-molekularno-biologijo-in-

nanobiotehnologijo/dogodki/mini-simpozij-piran-2013/

MiniSimpozij 2013

INTERAKCIJE MED PROTEINI IN MEMBRANAMI Morska biološka postaja, Piran, 6.9.2013

https://www.ki.si/odseki/d11-odsek-za-molekularno-biologijo-in- nanobiotehnologijo/dogodki/mini-simpozij-piran-2013/

MiniSimpozij 2014 MOLEKULSKE INTERAKCIJE

in Deset let Infrastrukturnega centra za raziskave molekulskih interakcij Oddelek za agronomijo, Biotehniška fakulteta, Univerza v Ljubljani, 3.12.2014

https://www.ki.si/odseki/d11-odsek-za-molekularno-biologijo-in- nanobiotehnologijo/dogodki/mini-simpozij-ljubljana-2014/

MiniSimpozij 2015

PROTEINSKE PORE, SEKVENCIRANJE IN BIOINFORMATIKA Kemijski inštitut, Ljubljana, 5.11.2015

https://www.ki.si/odseki/d11-odsek-za-molekularno-biologijo-in- nanobiotehnologijo/dogodki/mini-simpozij-2015/

MiniSimpozij 2016

ADVANCES IN MOLECULAR INTERACTION ANALYSIS National Institute of Chemistry, Ljubljana, 22.11.2016 https://www.ki.si/odseki/d11-odsek-za-molekularno-biologijo-in-

nanobiotehnologijo/dogodki/mini-simpozij-2016/

8

Abstract of the plenary lecture

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Structure and genome delivery mechanism of Staphylococcus aureus phage therapy agent phi812-K1 determined by cryo- electron microscopy

Jiří Nováček

jiri.novacek@ceitec.muni.cz

Central European Institute of Technology, Masaryk University, Brno, Czech Republic Worldwide occurrence of multidrug-resistant pathogenic bacteria has increased interest in alternative treatments including bacteriophage-based therapy.

Bacteriophage phi812 belongs to genus Twort-like virus, subfamily Spounavirinae and can infect at least 75% of Methicilin-resitant S. aureus strains (MRSA) and 95% of Methicillin-sensitive S. aureus strains. We have employed cryo-electron microscopy to determine structure and genome delivery mechanism for polyvalent staphylococcal backteriophage phi812-K1. Phi812-K1 has a 90 nm diameter isometric head and 240 nm long contractile tail ended by a double layered baseplate. The tail and baseplate of the native phage are dynamic. Therefore, a divide-and-conquer strategy was employed to separately determine the cryo-EM reconstructions of the individual phage parts.

Similarly to other phages from the family Myoviridae, host recognition and infection is accompanied with by tail sheath contraction with significant conformational change of baseplate. However, the release of the phage dsDNA is not governed only by tail sheath contraction. The data reveal presence of three species of phi812-K1 particles – a native virion, particles with contracted tail and DNA in the head, and phages with contracted tail and empty head. Structural analysis of these three species reveals that additional structural changes in the neck region are required after the tail contraction before the DNA is allowed to transfer to the host.

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Abstracts of short lectures

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Structural studies of flexible filamentous virus

Andreja Šink

, Martin Pólak

, Ion Gutiérrez-Aguirre

, Magda Tušek-Žnidarič

, Maja Ravnikar

, Gregor Anderluh

, Jiří Nováček

, Marjetka Podobnik

andreja.sink@ki.si

1Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia; ²Core Facility Cryo-electron Microscopy and Tomography, Central European Institute of Technology, Brno, Czech Republic;

3Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia

Plant viruses exist in all kinds of shapes and sizes. They have great impact in agriculture and can be used in applied science. We are studying a flexible filamentous plant virus, which is responsible for a huge damage on crop fields, moreover, it has a high potential for usage as a template in development of new pharmaceuticals or nanomaterials. To enable further studies of viral infectivity and scientific potential, it is important to determine its near-atomic three-dimensional structure.

Due to high flexibility, flexible filamentous viruses are not capable of forming protein crystals, which would be suitable for high-resolution X-ray crystallography. Fortunately, recent advances in cryo-electron microscopy can help us toward obtaining high- resolution three-dimensional structures of flexible filamentous particles. We are processing collected data of the virus using single particle analysis with helical reconstruction.

Schematic representation of flexible filamentous virus (A); infected plant (B); micrograph showing viral particles (C).

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Conventional transmission electron microscopy as a complementary tool in imaging of macromolecules and macromolecular assemblies

Nada Žnidaršič

, Magda Tušek Žnidarič

, Jasna Štrus

, Saša Rezelj

, Marjetka Podobnik

, Gregor Anderluh

nada.znidarsic@bf.uni-lj.si

1Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia; ²Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia; ³Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia

Imaging is an integrative part of biological structures characterization and transmission electron microscopy (TEM) enables imaging at the best resolution available. TEM is a versatile method, offering different techniques for specimen preparation and visualization. Concerning imaging of isolated macromolecules or macromolecular assemblies, negative staining has been used for years and it is still a valuable tool, as preparation procedure is quick, a small amount of the sample is needed and high contrast imaging is achieved. Thus, it is advantageous for evaluating isolation/purification processes, for visualization of smaller particles and is indispensable in immunolocalization. However, staining and drying introduce artefacts that we have to take into account at interpretation and some can be partially prevented. State of the art TEM are cryo-electron microscopy methods, including single particle analyses and tomography. Complementary imaging approaches should be used in combination with quantitative biophysical/biochemical techniques to reveal adequate structural and functional information on macromolecules.

Transmission electron microscopy image of listeriolysin O pores on liposome.

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Negative staining method for transmission electron

microscopy of biological samples – the player in the team Magda Tušek Žnidarič

, Polona Kogovšek

, Nada Žnidaršič

magda.tusek.znidaric@nib.si

1Department of Biotechnology and System Biology, National Institute of Biology, Ljubljana, Slovenia; ²Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia

A huge number of microscopic methods and their variations were developed in last 30 years. Negative staining method is simple, but very useful for visualisation of small biological particles in the solution with transmission electron microscope (TEM). In combination with other methods, it represents a powerful tool in different research fields.

In parallel to biochemical methods, like different separation and spectroscopic techniques, the changes in protein conformation could be followed and TEM gives a great contribution to determine protein structure. Many diseases base on protein misfolding, aggregation and fibrillation (Fig. A) and one of model proteins to the study protein fibrillation is human stefin B¹.

Adeno-associated viruses (Fig. B) represent promising vehicles for delivering genetic material in gene therapy. During production of clinical grade biomolecules, it is of great importance to check concentration and purity in each step and only TEM enable us to detect everything present in the sample.

Biological samples prepared with negative staining method and observed with transmission electron microscope. A. Fibrilated protein. B. Adeno associated viruses.

Reference:

(1) Žerovnik E. et al. (2006) FEBS J. 273, 4250–4263.

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Advanced transmission electron microscopy at NIC

Elena Tchernychova, Goran Dražić, Francisco Ruiz Zepeda

Department for Materials Chemistry, National Institute of Chemistry, Ljubljana, Slovenia “The devil is in the detail”. Transmission electron microscopy (TEM) equipped with simultaneous visual and analytical capabilities represents one of the finest performers in the field of investigation of structural and chemical details in materials. State of the art scanning TEM (STEM) instruments fortified with probe spherical aberration correctors allow these days a point-to-point resolution of 0.8 Å and less. This lies below the lattice spacing of a large number of crystalline materials, allowing the investigation of atomic species at almost “personal” level. In the past 4 years we used the opportunities of such atomic resolution STEM (AR-STEM) instrument installed at our institute to shed the light on the details of catalytic nanomaterials, Li-ion battery cathode materials, polymers, various ceramic nanostructures, etc. Our aim is to connect the chemical and structural peculiarities observed in the nano-world with the macroscopic properties of the investigated material. The scientific problems related to the life sciences tackled by our microscope will also be addressed in the presentation.

15

Electron tomography of cellular structures

Samo Hudoklin

samo.hudoklin@mf.uni-lj.si

Institute of cell biology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia Biological processes ongoing in the organisms are critically depended on spatio- temporal distribution and interactions of macromolecules, assembled into cellular compartments. Microscopic methods, in particular transmission electron microscopy (TEM), are the only methods that have resolving power required to provide information about the presence and location of macromolecules and cellular compartments within the cells. However, thickness (30-80 nm) of classical TEM sections reduces the information about inherently three-dimensional cellular compartments into two- dimensional images. Electron tomography is a microscopic method, which overcomes this problem and provides three-dimensional spatial organization of cellular compartments at nanometre resolution. Electron tomography is implemented at the Institute of Cell Biology, Faculty of Medicine, together with the cryo-fixation methods and other methods, which are crucially important for the complete and competent preparation of biological samples closes to their in vivo conditions. In the talk, workflow and results obtained by electron tomography on urothelial tissue will be presented.

Three-dimensional model of fusiform vesicles obtained by the method of electron tomography.

Fusiform vesicles are characteristic transport vesicles of differentiated urothelial cells, which contribute to the permeability barrier of human urinary bladder. Bar: 250 nm.

16

Structure-based drug design: from selective butyrylcholinesterase inhibitors towards multifunctional anti- Alzheimer ligands

Damijan Knez,

Urban Košak,

Boris Brus,

Anja Pišlar,

Nicolas Coquelle,

Jurij Stojan,

Janko Kos,

Jacques-Philippe Colletier,

Stanislav Gobec

damijan.knez@ffa.uni-lj.si

1Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia; ²Institut de Biologie Structurale (IBS), University Grenoble Alpes, Grenoble, France; ³Insitute of Biochemistry, Faculty of medicine, University of Ljubljana, Ljubljana, Slovenia

Alzheimer’s disease (AD) is a complex disorder characterized by progressive and chronic deterioration of the memory and other cognitive functions. Numerous factors are involved in AD progression: oxidative stress, increased activity of monoamine oxidase B (MAO-B), loss of metal homeostasis, and a severe decrease in levels of acetylcholine.¹ In the late stages of AD, enzyme butyrylcholinesterase (BChE) takes over the acetylcholine breakdown, which makes it a promising target in the therapy of AD.² Piperidine based selective BChE inhibitor identified in a structure-based virtual screening³ was used as a starting point for on-target activity optimization and further on to design two series of multifunctional ligands with metal chelating properties, antioxidant activity and neuroprotective properties against amyloid β fibrils.⁴ Dual BChE/MAO-B inhibitors with N-propargylpiperidine scaffold were also developed.⁵ The resolved crystal structures of several inhibitors in complex with BChE reveal their binding mode and explain their low micromolar to picomolar inhibitory potencies.

References:

(1) a) Querfurth H.W. et al. (2010) N. Engl. J. Med., 362, 329; b) Winbald B. et al. (2016) Lancet Neurol., 15, 455.

(2) a) Greig N.H. et al., (2001) Curr. Med. Res. Opin. 17, 159; b) Greig N.H. et al. (2005) Proc. Natl. Acad. Sci.

USA, 102, 17213; c) Mushtaq G. et al. (2014) CNS Neurol. Disord. Drug Targets, 13, 1432. (3) Brus B. et al.

(2014) J. Med. Chem., 57, 8167. (4) a) Košak U. et al. (2016) Sci. Rep., 6, 39495; b) Košak U. et al., submitted for publication; c) Knez D. et al. (2015) Bioorg. Med. Chem., 23, 4442; d) Knez D. et al., manuscript in preparation.

(5) Košak U. et al. (2017) Bioorg. Med. Chem., 25, 633.

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Rfree: a dinosaur marked for extinction?

Dušan Turk

Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia

Over fitting in refinement is in macromolecular crystallography controlled by R-free in a cross validation procedure. However, the R-free concept has its limitations: it does not allow the use of all data in refinement and map calculations, the presence of NCS makes it impossible to decouple the independence of TEST set reflections from the rest of the data, and the exchange of the TEST set can result in a considerably different gap between R-work and R-free, the distribution of errors in model is not random but correlated. To overcome the limitations of the R-free concept we developed an approach that uses the WORK set to calculate the phase error estimates in the ML refinement from simulating the model errors. We call it ML Free Kick refinement.

This approach of calculation of error estimates is superior to the cross validation approach in accuracy and phase errors of resulting structures.

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Macromolecular machines involved in DNA replication: an integrated structural biology approach

Silvia Onesti

silvia.onesti@elettra.trieste.it

Elettra - Sincrotrone Trieste, Area Science Park, Trieste, Italy

The CMG (Cdc45–MCM–GINS) complex is the eukaryotic replicative helicase, the enzyme that unwinds double-stranded DNA at replication forks. Over the last few years we have carried out biochemical and structural studies on MCM, GINS and Cdc45 which provided important insights into the three dimensional architecture of the complex, its function and evolution. We have recently focussed our attention to the archaeal homologue of Cdc45: the eukaryotic Cdc45 shows sequence and structural similarity to protein belonging to the RecJ family of exonucleases. We have obtained a number of crystal structure of archaeal Cdc45-RecJ, with and without nucleotides and oligonucleotides, which shed light on the exonuclease function and provide a framework to understand the evolution of Cdc45 and the CMG complex.

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Tail and intermodule linker flexibility of testicans explored by SAXS

Miha Pavšič

miha.pavsic@fkkt.uni-lj.si

Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia

Testicans, modular proteoglycans of the extracellular matrix (ECM) of various tissues, play important role in tissue formation and remodeling – they stimulate neurite outgrowth, promote cell migration, and regulate activity of extracellular proteases.

Similarly to several other components of the ECM they are believed to contain flexible regions making them notoriously difficult to study by conventional high-resolution structural approaches like X-ray crystallography. Here, we employed small angle X-ray scattering (SAXS) to gain insight into the flexibility of the testican core protein. Results confirmed the hypothesis that both N- and C-terminal tails are disordered, and indicated that short flexible regions are also found within the central part. Therefore, the follistatin-like (FS), extracellular calcium-binding (EC), and thyroglobulin type-1 domain (TY) do not form a completely compact globule as previously speculated. The observed disorder could thus provide the necessary structural plasticity for both ECM organization as well as interaction with various proteins within different tissues.

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Coiled-coil protein origami cages (capable of in vivo self- assembly)

Ajasja Ljubetič

, Jana Aupič

, Igor Drobnak

, Tomaž Pisanski

, Fabio Lapenta

, Žiga Strmšek

, Helena Gradišar

, Roman Jerala

roman.jerala@ki.si

1Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia; ²EN-FIST Centre of Excellence, Ljubljana, Slovenia; ³Faculty of Mathematics and Physics, University of Ljubljana, Slovenia

Polypeptides are nature’s most versatile nano-machines, capable of efficient self- assembly. A similar strategy as in DNA nanotechnology can be applied to construct protein origami cages using coiled-coil (CC) dimers as building modules. The developing field of CC protein origami^1,2 would benefit from software to ease the creation of novel origamis.

We have created CoCoPOD, a coiled-coil protein origami design platform, for automated design of arbitrary polyhedral CC cages. The end result of the design is a single-chain amino acid sequence, as well as an ensemble of probable 3D models.

CoCoPOD enabled the design of tetrahedra, square pyramids and a triangular prism, which contains more than 700 amino acid residues³.

The correct shape of the designs was confirmed by solution SAXS, TEM and biophysical analysis. Cages were produced and self-assembled in bacteria, as well as in mammalian cells and in animals, without causing inflammation or other adverse pathological effects.

Next generation CC polyhedra. Tetrahedron, square pyramid and triangular prism designs are presented. For each polyhedral the topology, i.e. the connectivity of segments, (upper left) a 3D model (upper right) and the linear order of segments are shown.

References:

(1) Gradišar H. et al. (2013) Nat. Chem. Biol., 9, 362–366; (2) Drobnak I. et al. (2016) Designed Protein Origami, in Protein-based Engineered Nanostructures (Springer) 7–27; (3) Ljubetič A. et al. (2017) Nat Biotech, doi:10.1038/nbt.3994.

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