Cover image for Vol. 107 Issue 8

Edited By: Hilary J. Crichton

Online ISSN: 1097-0282

Associated Title(s): Peptide Science

Virtual Issues

Recent Reviews

Published: November 2014

Review collagen-based biomaterials for wound healing
Sayani Chattopadhyay and Ronald T. Raines

Monitoring of post-translational modification dynamics with genetically encoded fluorescent reporters
Fabian Hertel and Jin Zhang

Strategies for profiling native S-nitrosylation
Jaimeen D. Majmudar and Brent R. Martin

Chemical biology approaches to study protein cysteine sulfenylation
Jia Pan and Kate S. Carroll

Orphan PTMs: Rare, yet functionally important modifications of cysteine
D. Alexander Shannon and Eranthie Weerapana

Chemical strategies to understand the language of ubiquitin signaling
Caroline E. Weller, Meagan E. Pilkerton and Champak Chatterjee

Chemical and biological methods to detect post-translational modifications of arginine
Daniel J. Slade, Venkataraman Subramanian, Jakob Fuhrmann and Paul R. Thompson Ignacio Tinoco Jr., Hee-Kyung Kim and Shannon Yan

Published: 2013

Frameshifting dynamics
Ignacio Tinoco Jr., Hee-Kyung Kim and Shannon Yan

Rearranging RNA structures at 75°C? toward the molecular mechanism and physiological function of the thermus thermophilus DEAD-box helicase hera
Dagmar Klostermeier

A personal perspective on chemistry-driven RNA research
Ronald Micura, Christoph Kreutz and Kathrin Breuker

Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water
David E. Draper

Fundamental interactions in RNA: Questions answered and remaining
Douglas H. Turner

Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model
Steve P. Meisburger, Julie L. Sutton, Huimin Chen, Suzette A. Pabit, Serdal Kirmizialtin, Ron Elber and Lois Pollack

Long-range mapping of DNA
Donald M. Crothers

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment
Jiří Šponer, Judit E. Šponer, Arnošt Mládek, Petr Jurečka, Pavel Banáš and Michal Otyepka

Twenty-five years of nucleic acid simulations
Thomas E. Cheatham III and David A. Case

A historical account of hoogsteen base-pairs in duplex DNA
Evgenia N. Nikolova, Huiqing Zhou, Federico L. Gottardo, Heidi S. Alvey, Isaac J. Kimsey and Hashim M. Al-Hashimi

Fifty years of DNA “Breathing”: Reflections on old and new approaches
Peter H. von Hippel, Neil P. Johnson and Andrew H. Marcus

Biopolymers and the fellowship of DNA rings
James C. Wang

Physical chemistry of nucleic acids and their complexes
Rodolfo Ghirlando and Gary Felsenfeld

Advances in turbulent mixing techniques to study microsecond protein folding reactions
Sagar V. Kathuria, Alexander Chan, Rita Graceffa, R. Paul Nobrega, C. Robert Matthews, Thomas C. Irving, Blair Perot and Osman Bilsel

Under-folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis
Vladimir N. Uversky

Protein folding and unfolding under force
Bharat Jagannathan and Susan Marqusee

ATP-driven molecular chaperone machines
Daniel K. Clare and Helen R. Saibil

Story in a sample—the potential (and limitations) of cryo-electron microscopy applied to molecular machines
Joachim Frank

NMR-profiles of protein solutions
Bill Pedrini, Pedro Serrano, Biswaranjan Mohanty, Michael Geralt and Kurt Wüthrich

Revealing structural views of biology
David S. Goodsell, Stephen K. Burley and Helen M. Berman

Structural biology computing: Lessons for the biomedical research sciences
Andrew Morin and Piotr Sliz

Synthesis of Glycans and Glycopolymers Through Engineered Enzymes
Zachary Armstrong and Stephen G. Withers

Exploration of Sialic Acid Diversity and Biology Using Sialoglycan Microarrays
Lingquan Deng, Xi Chen and Ajit Varki


Chromatin structure outside and inside the nucleus
Rodolfo Ghirlando and Gary Felsenfeld

Hydration shells with a pinch of salt
Giuseppe Zaccai

Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding
Allen P. Minton

ATP and ADP actin states
Dmitri S. Kudryashov and Emil Reisler

Interaction of oil sands tailings particles with polymers and microbial cells: First steps toward reclamation to soil
Gerrit Voordouw

Evolution of the concept of conformational dynamics of enzyme functions over half of a century: A personal view
Péter Závodszky and István Hajdú

Studying and polishing the PDB's macromolecules
Jane S. Richardson and David C. Richardson

Abstracting knowledge from the protein data bank
Nicholas Furnham, Roman A. Laskowski and Janet M. Thornton

The impact of influenza hemagglutinin fusion peptide length and viral subtype on its structure and dynamics
Justin L. Lorieau, John M. Louis and Ad Bax

Sweet entanglements—protein: Glycan interactions in two HIV-inactivating lectin families
Leonardus M. I. Koharudin and Angela M. Gronenborn

A primer in macromolecular linguistics
David B. Searls

The future of the protein data bank
Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura and John L. Markley

Histone acetyltransferases: Rising ancient counterparts to protein kinases
Hua Yuan and Ronen Marmorstein

HDAC8 substrates: Histones and beyond
Noah A. Wolfson, Carol Ann Pitcairn and Carol A. Fierke

The many facets of MLL1 regulation
Pamela Zhang, Elisa Bergamin and Jean-François Couture

STUbLs in chromatin and genome stability
Renee Garza and Lorraine Pillus


Macromolecular structure modeling from 3D EM using VolRover 2.0
Qin Zhang, Radhakrishna Bettadapura, Chandrajit Bajaj

Implications of protein structure instability: From physiological to pathological secondary structure
Alyona Sukhanova, Simon Poly, Anton Shemetov, Igor Bronstein, Igor Nabiev

The role of terminal domains during storage and assembly of spider silk proteins
Lukas Eisoldt, Christopher Thamm, Thomas Scheibel

Structure of silk by raman spectromicroscopy: From the spinning glands to the fibers
Thierry Lefèvre, François Paquet-Mercier, Jean-François Rioux-Dubé, Michel Pézolet

Extrusion based rapid prototyping technique: An advanced platform for tissue engineering scaffold fabrication
M. Enamul Hoque, Y. Leng Chuan, Ian Pashby


The effects of shear flow on protein structure and function
Innocent B. Bekard, Peter Asimakis, Joseph Bertolini, Dave E. Dunstan

Minireview: Structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering
Sagar V. Kathuria, Liang Guo, Rita Graceffa, Raul Barrea, R. Paul Nobrega, C. Robert Matthews, Thomas C. Irving, Osman Bilsel

Invited review: Probing the structures of muscle regulatory proteins using small-angle solution scattering
Yanling Lu, Cy M. Jeffries, Jill Trewhella

Forcing a connection: Impacts of single-molecule force spectroscopy on in vivo tension sensing
Michael D. Brenner, Ruobo Zhou, Taekjip Ha

PALM and STORM: Unlocking live-cell super-resolution
Ricardo Henriques, Caron Griffiths, E. Hesper Rego, Musa M. Mhlanga

How to quantify protein diffusion in the bacterial membrane
Siet M. J. L. van den Wildenberg, Yves J. M. Bollen, Erwin J. G. Peterman

Erratum: “Review: Optical Mapping of DNA: Single-Molecule-Based Methods for Mapping Genomes”
Robert K. Neely, Jochem Deen, Johan Hofkens

DNA and chromatin imaging with super-resolution fluorescence microscopy based on single-molecule localization
Cristina Flors

De novo design of a,ß-didehydrophenylalanine containing peptides: From models to applications
Madhvi Gupta, Virander S. Chauhan

Diterpenoid biopolymers: New directions for renewable materials engineering
Matthew L. Hillwig, Francis M. Mann, Reuben J. Peters

Protein–protein interactions in transcription: A fertile ground for helix mimetics
Danielle A. Guarracino, Brooke N. Bullock, Paramjit S. Arora


Recent developments in bisintercalator natural products
Olga E. Zolova, Ahmed S. A. Mady, Sylvie Garneau-Tsodikova

Recent advancements in the biosynthetic mechanisms for polyketide-derived mycotoxins
Justin Huffman, Ryan Gerber, Liangcheng Du

Biosynthesis of lovastatin and related metabolites formed by fungal iterative PKS enzymes
Chantel D. Campbell, John C. Vederas

Vibrational spectroscopic studies of newly developed synthetic biopolymers
Rajan K. Bista1,Reinhard F. Bruch1, Aaron M. Covington

Hsp90 and co-chaperones twist the functions of diverse client proteins
Abbey Zuehlke, Jill L. Johnson

Hsp70 molecular chaperones and Parkinson's disease
Stephan N. Witt

Interplay between protein homeostasis networks in protein aggregation and proteotoxicity
Peter M. Douglas, Douglas M. Cyr

Identifying protein stabilizing ligands using GroEL
Subhashchandra Naik, Inamul Haque1, Nick Degner, Boris Kornilayev, Gregory Bomhoff, Jacob Hodges, Ara-Azad Khorassani, Hiroo Katayama, Jill Morris, Jeffery Kelly, John Seed, Mark T. Fisher

Structure and function of the molecular chaperone Hsp104 from yeast
Valerie Grimminger-Marquardt, Hilal A. Lashuel

Revisiting the neighbor exclusion model and its applications
Marcio S. Rocha

2007 - 2009

Introduction: This landmark first Virtual Issue of Biopolymers presents a collection of review and special topic articles that have appeared in the Journal since its re-launch in January 2007. The collection covers a range of contemporary topics in biophysical chemistry and chemical biology by leading international authors and is representative of the expanded scope of Biopolymers and the editorial commitment to showcasing the most important studies in all facets of biopolymers research.

Nanofluidic structures for single bimolecule fluorescent detection
Mannion, J.T.; Craighead, H.G.

Mechanisms of DNA binding determined in optical tweezers experiments
McCauley, M.J.; Williams, M.C.

Single molecule studies of molecular diffusion in cellular membranes: Determining membrane structure
Ritchie, K.; Spector, J.

A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single-molecule FRET
Munro, J.B.; Vaiana, A.; Sanbonmatsu, K.Y.; Blanchard, S.C.

Optical tweezers experiments resolve distinct modes of DNA-protein binding
McCauley, M.J.; Williams, M.C.

Molecular dynamics simulations of RNA: An in silico single molecule approach
McDowell, S.D.; Spacková, N.; Sponer, J.; Walter, N.G.

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
Roccatano, D.; Barthel, A.; Zacharias, M.

Continuum molecular electrostatics, salt effects, and counterion binding - A review of the Poisson-Boltzmann theory and its modifications
Grochowski, P.; Trylska, J.

Peptidic modulators of protein-protein interactions: Progress and challenges in computational design
Rubinstein, M.; Niv, M.Y.

Role of GTPases in ribosome assembly
Karbstein, K.

Do electrostatic interactions destabilize protein-nucleic acid binding?
Qin, S.; Zhou, H.X.

NMR studies of dynamics in RNA and DNA by 13C relaxation
Shajani, Z.; Varani, G.

Time-resolved NMR studies of RNA folding
Fürtig, B.; Buck, J.; Manoharan, V.; Bermel, W.; Jäschke, A.; Wenter, P.; Pitsch, S.; Schwalbe, H.

Review NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings
Getz, M.; Sun, X.; Casiano-Negroni, A.; Zhang, Q.; Al-Hashimi, H.M.

Recent advances in DNA catalysis
Höbartner, C.; Silverman, S.K.

Applications of isothermal titration calorimetry in RNA biochemistry and biophysics
Feig, A.L.

Focus on function: Single molecule RNA enzymology
Ditzler, M.A.; Alemán, W.A.; Rueda, D.; Walter, N.G.

Structure-function relationships in RNA and RNP enzymes: Recent advances
Hoogstraten, C.G.; Sumita, M

Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis
Smith, J.K.; Hsieh, J.; Fierke, C.A.

Review fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation
Van Orden, A.; Jung, J.

Disruption of the HIV-1 protease dimer with interface peptides: Structural studies using NMR spectroscopy combined with [2-13C]-Trp selective labeling
Frutos, S.; Rodriguez-Mias, R.A.; Madurga, S.; Collinet, B.; Reboud-Ravaux, M.; Ludevid, D.; Giralt, E.

Cryptides: Functional cryptic peptides hidden in protein structures
Ueki, N.; Someya, K.; Matsuo, Y.; Wakamatsu, K.; Mukai, H.

Switch-peptides as folding precursors in self-assembling peptides and amyloid fibrillogenesis
Tuchscherer, G.; Chandravarkar, A.; Camus, M.S.; Bérard, J.; Murat, K.; Schmid, A.; Mimna, R.; Lashuel, H.A.; Mutter, M.

Fmoc-based solid-phase synthesis of GPR54-agonistic pentapeptide derivatives containing alkene- and fluoroalkene-dipeptide isosteres
Tomita, K.; Narumi, T.; Niida, A.; Oishi, S.; Ohno, H.; Fujii, N.

Targeting protein-protein interactions: Lessons from p53/MDM2
Murray, J.K.; Gellman, S.H.

Studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination
Zoppellaro, G.; Bren, K.L.; Ensign, A.A.; Harbitz, E.; Kaur, R.; Hersleth, H.P.; Ryde, U.; Hederstedt, L.; Andersson, K.K.

Collagen scaffolds for tissue engineering
Glowacki, J.; Mizuno, S.

Triple-helical peptides: An approach to collagen conformation, stability, and self-association
Brodsky, B.; Thiagarajan, G.; Madhan, B.; Kar, K.

Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41
Almog, O; Kogan, A.; de Leeuw, M.; Gdalevsky, G.Y.; Cohen-Luria, R.; Parola, A.H.

Roles of beta-turns in protein folding: From peptide models to protein engineering
Marcelino, A.M.C.; Gierasch, L.M.

Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases
Whitmore, L.; Wallace, B.A.

From helix-coil transitions to protein folding
Scheraga, H.A.

Recent progress in the field of glycopeptide synthesis
Hojo, H.; Nakahara, Y

Higher order structure of (1,3)-beta-D-glucans and its influence on their biological activities and complexation abilities
Sletmoen, M.; Stokke, B.T.

Review: An overview about the structure-function relationship of marine sulfated homopolysaccharides with regular chemical structures
Pomin, V.H.

Quantum dots and peptides: A bright future together
Zhou, M.; Ghosh, I.

On the use of ESI-QqTOF-MS/MS for the comparative sequencing of nucleic acids
Oberacher, H.; Pitterl, F.