BIOPHYS. J.-PyContact

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations

Maximilian Scheurer, Peter Rodenkirch, Marc Siggel, Rafael C. Bernardi, Klaus Schulten, Emad Tajkhorshid, Till Rudack

1.NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
2.Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois
3.Department of Biophysics, Ruhr University Bochum, Bochum, Germany
DOI: https://doi.org/10.1016/j.bpj.2017.12.003
Copyright © 2017 Elsevier Inc. except certain content provided by third parties

Protein contacts are vital in many biological processes. PyContact is a novel tool developed to identify, analyze, and visualize these contacts in molecular dynamics simulations.

Science-Single-stranded DNA and RNA origami

Single-stranded DNA and RNA origami

Dongran Han1,2,*, Xiaodong Qi3,4,*, Cameron Myhrvold1,2, Bei Wang2,5, Mingjie Dai1,2, Shuoxing Jiang3,4, Maxwell Bates6, Yan Liu3,4, Byoungkwon An6,†, Fei Zhang3,4,†, Hao Yan3,4,†, Peng Yin1,2,†
1.Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
2.Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
3.Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA.
4.School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA.
5.Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
6.BioNano Research Group, Autodesk Life Sciences, Pier 9, San Francisco, CA 94111, USA.

Science  15 Dec 2017:
Vol. 358, Issue 6369, eaao2648
DOI: 10.1126/science.aao2648
© 2017 American Association for the Advancement of Science. All rights reserved. AAAS is a partner of HINARI, AGORA, OARE, CHORUS, CLOCKSS, CrossRef and COUNTER. Science ISSN 1095-9203

Unimolecular folding of single-stranded DNA and RNA origami into user-specified shapes.

3D animation:

JACS-Cellulosomal Scaffoldin Mechanics

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics

Tobias Verdorfer†, Rafael C. Bernardi‡, Aylin Meinhold†, Wolfgang Ott†, Zaida Luthey-Schulten‡§, Michael A. Nash*∥⊥, and Hermann E. Gaub† 
† Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
‡ Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Department of Chemistry, University of Basel, 4056 Basel, Switzerland
Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zurich), 4058 Basel, Switzerland
J. Am. Chem. Soc., 2017, 139 (49), pp 17841–17852
DOI: 10.1021/jacs.7b07574
Publication Date (Web): October 23, 2017
Copyright © 2017 American Chemical Society

The force induced unfolding behavior of all cohesins from the scaffoldin ScaA was successfully characterized by combining in vitro and in silico single-molecule force spectroscopy.

Science-A cargo-sorting DNA robot

A cargo-sorting DNA robot

Anupama J. Thubagere1, Wei Li1, Robert F. Johnson1, Zibo Chen1, Shayan Doroudi2, Yae Lim Lee3, Gregory Izatt2,4, Sarah Wittman2, Niranjan Srinivas4, Damien Woods2,*, Erik Winfree1,2,4, Lulu Qian1,2,†
1. Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA.
2. Computer Science, California Institute of Technology, Pasadena, CA 91125, USA.
3. Electrical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
4. Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA.
DOI: 10.1126/science.aan6558
© 2017 American Association for the Advancement of Science. All rights Reserved. AAAS is a partner of HINARI, AGORA OARE, PatientInform, CHORUS, CLOCKSS, CrossRef and COUNTER. Science ISSN 1095-9203.

Single-stranded DNA robots with three modular functional domains were designed to move over the surface of a DNA origami sheet and sort molecular cargoes with no additional power input.

Adv. Funct. Mater-Micromotors

Bioinspired Spiky Micromotors Based on Sporopollenin Exine Capsules

Hong Wang1, Michael G. Potroz2, Joshua A. Jackman2, Bahareh Khezri1, Tijana Marić1, Nam-Joon Cho2,3 and Martin Pumera1,*
1. Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
2. School of Materials Science and Engineering and Centre for Biomimetic Sensor Science, Nanyang Technological University, Singapore, Singapore
3. School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
DOI: 10.1002/adfm.201702338
© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

A bioinspired spiky micromotor was designed based on sporopollenin exine capsules where bubble generated on the surface propels the capsules to transport cargo or decontaminate heavy metals.

Nano Letters-Mapping Mechanical Force Propagation through Biomolecular Complexes

Mapping Mechanical Force Propagation through Biomolecular Complexes

Constantin Schoeler†, Rafael C. Bernardi‡, Klara H. Malinowska†, Ellis Durner†, Wolfgang Ott†§, Edward A. Bayer∥, Klaus Schulten‡⊥, Michael A. Nash*†, and Hermann E. Gaub†
† Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
‡ Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
§ Center for Integrated Protein Science Munich (CIPSM), University of Munich, 81377 Munich, Germany
∥ Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
⊥ Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
Nano Lett., 2015, 15 (11), pp 7370–7376
DOI: 10.1021/acs.nanolett.5b02727
Publication Date (Web): August 11, 2015
Copyright © 2015 American Chemical Society
Single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations revealed force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex.

Cell Systems-Modular Viral Scaffolds for Targeted Bacterial Population Editing

Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing

Hiroki Ando1, Sebastien Lemire1, Diana P. Pires1,2, Timothy K. Lu1
1 Department of Electrical Engineering and Computer Science and Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
2 Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
Cell Systems, Volume 1, Issue 3, 23 September 2015, Pages 187–196
DOI: http://dx.doi.org/10.1016/j.cels.2015.08.013
Copyright © 2015 Elsevier B.V. or its licensors or contributors. ScienceDirect® is a registered trademark of Elsevier B.V.
A synthetic biology strategy to modulate phage host ranges by engineering phage genomes in Saccharomyces cerevisiae. This innovative approach could potentially accelerate phage biology studies and enable new technologies for bacterial population editing.