Article
Biochemistry & Molecular Biology
Mohammed A. Abosheasha, Toru Itagaki, Yoshihiro Ito, Motoki Ueda
Summary: The LxxxLxxxL sequence is crucial for nanotube self-assembly, as evidenced by the formation of nanotubes with different diameters and the fabrication of double-layer nanotubes by combining two types of nanotubes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Prasun Kumar, Neil G. Paterson, Jonathan Clayden, Derek N. Woolfson
Summary: The alpha-helix is important in structural biology and protein folding. This study shows that synthetic peptide assemblies can be built from 3(10)-helices, which are less common in natural proteins. The research provides principles and rules for designing in this unexplored region of protein structure.
Article
Chemistry, Physical
Leena Majumder, Nayim Sepay, Biswadip Banerji
Summary: Self-assembled structures derived from short peptides, like the dityrosine-based short peptide (TP) studied in this research, have great potential in various domains. Through spectroscopic studies and single crystal X-ray analysis, it was confirmed that TP adopted a B-sheet pattern and further self-assembled into B-sheet-promoted helical architectures. This is the first crystallographic report of this kind of short peptide adopting B-sheet-promoted helical structures. CD spectroscopy, NMR study, and other analyses also supported the self-assembly phenomenon of TP. These small peptide units mimicking protein secondary structures could be of pivotal significance.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Polymer Science
Brandon R. Clarke, Gregory N. Tew
Summary: We report the synthesis of novel poly(ethylene glycol) and poly(dimethyl siloxane) bottlebrush amphiphilic polymer co-networks, and demonstrate the ability to control their crystallinity and moduli by varying the volume fraction of PEG. These bottlebrush networks represent an unexplored architecture for the field of amphiphilic polymer co-networks.
Article
Biochemistry & Molecular Biology
Eloise Masquelier, Sheng-Ping Liang, Lior Sepunaru, Daniel E. Morse, Michael J. Gordon
Summary: The reversible electrochemical triggering of polylysine conformational transition was achieved at a Pt electrode, allowing for easy distinction of different reduction processes. In situ UV absorbance and circular dichroism spectroscopies were used to track the evolution of alpha-helix formation, while isotope experiments confirmed direct electroreduction as the cause of subsequent alpha-helix formation. The site-selective electrochemistry and optical methodologies present potential for studying and controlling dynamic structural evolution in biomolecular systems.
BIOELECTROCHEMISTRY
(2022)
Article
Chemistry, Physical
Ake Andersson, Vasyl Yatsyna, Mathieu Linares, Anouk Rijs, Vitali Zhaunerchyk
Summary: We investigate the gas-phase structure of the neutral pentaalanine peptide using supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. The molecule assumes multiple stable conformations, mainly of two structure types, with the most stable conformation featuring a C5 ring at the N-terminus and a 310-helix backbone with two beta-turns. The conformational preferences of pentaalanine are also evaluated using Born-Oppenheimer molecular dynamics, revealing a systematic frequency shift caused by a nonzero simulation time step.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Review
Chemistry, Medicinal
Sergio Algar, Mercedes Martin-Martinez, Rosario Gonzalez-Muniz
Summary: Researchers have developed a variety of non-peptide alpha-helix mimetics to modulate protein-protein interactions, with the potential to stabilize or disrupt therapeutically relevant PPIs. The diverse chemical structures and substituents allow for a wide range of choices in research, offering new opportunities for future studies on protein interactions.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Physical
Sridip Parui, Biman Jana
Summary: The study examines the effect of cold temperature on the alpha-helical region of the Trp-cage miniprotein using molecular dynamics simulations, observing a helix-to-helix transition below 230K primarily driven by water-water interactions. This transition may lead to cold denaturation of the protein. Unlike Trp-cage, the antifreeze protein AFP has a helical arrangement that facilitates hydrogen bonding with surrounding ice-like water molecules, crucial for its antifreeze activity.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Polymer Science
Luis A. Baptista, Yani Zhao, Kurt Kremer, Debashish Mukherji, Robinson Cortes-Huerto
Summary: We propose a mechanism that explains the folding of polyalanine in aqueous urea. Our simulations show that a balance between urea-residue dipole interactions and hydrogen bonds determines the solvation properties and structure of the polypeptide. This mechanism explains the tendency of alanine-rich systems to form secondary structures at low and intermediate urea concentrations, and the unfolding of helix structures at high urea concentrations. These findings highlight the importance of dipole-dipole interactions for understanding protein solvation.
Article
Chemistry, Applied
Liang Yao, Jiang Xu, Liwei Zhang, Lei Liu, Lei Zhang
Summary: The research demonstrates that the C6M1 peptide significantly enhances the tolerance of anthocyanin to increases in pH, metallic ions, and high temperatures, while also maintaining the intrinsic ability of anthocyanin to scavenge free radicals.
FOOD HYDROCOLLOIDS
(2021)
Article
Chemistry, Multidisciplinary
Young-Hee Shin, Hyunjun Yang
Summary: The systematic incorporation of ring-constrained beta- and gamma-amino acid residues into alpha-helix mimetics results in stable helical secondary structures. The constructed alpha/beta/gamma-helical peptidomimetics effectively mimic BH3 helical domains and exhibit excellent resistance against proteolytic digestion. Further optimization of the alpha/beta/gamma-backbone strategy is expected to significantly enhance the utility of functional alpha/beta/gamma-peptidomimetics, particularly due to their notable stability against proteolysis.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Peng Teng, Mengmeng Zheng, Darrell Cole Cerrato, Yan Shi, Mi Zhou, Songyi Xue, Wei Jiang, Lukasz Wojtas, Li-June Ming, Yong Hu, Jianfeng Cai
Summary: This study demonstrated the solid-state right-handed helical propensity of the 4(13)-helix of L-alpha/L-sulfono-gamma-AA peptides, even as short as 11-mer, using high-resolution X-ray single crystallography. The atomic level folding conformation of the foldamers was elucidated by 2D NMR and circular dichroism, showing that the helical handedness of this class of foldamer is controlled by the chirality of their chiral side chains.
COMMUNICATIONS CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Andrea Mosseri, Maria Sancho-Albero, Marilisa Leone, Donatella Nava, Francesco Secundo, Daniela Maggioni, Luisa De Cola, Alessandra Romanelli
Summary: This study reports the formation of homogeneous chiral fibers through self-assembly of peptide nucleic acids. Nucleobases play a key role in determining the morphology and chirality of the fibers. By spectroscopic characterization and microscopy studies, a structural model consistent with the experimental evidence was obtained.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Polymer Science
Tao Wen, Yuting Gao, Jiajia Zhou, Jie Qiu, Shuo Wang, Joachim Loos, Dujin Wang, Xia Dong
Summary: In this study, we introduce a simple method for fast fabrication of porous films and coatings of long-chain polyamides through a nonconventional evaporation induced phase separation. The amphiphilic nature of polyamide 12 allows it to be dissolved in a mixture of high-polarity and low-polarity solvents, leading to the formation of porous structures within 1 min through sequential and fast evaporation. We also investigate the dependence of pore structures on the composition of solutions and demonstrate the applicability of our approach to other long-chain polycondensates. Our findings provide valuable insights into the fabrication of porous materials using amphiphilic polymers.
Article
Chemistry, Multidisciplinary
Diego Navarro-Barreda, Cesar A. Angulo-Pachon, Francisco Galindo, Juan F. Miravet
Summary: The anionic azobenzene-appended derivative of l-ValylGlycine self-assembles into nanotubes in water. Irradiation with 365 nm light triggers trans-cis isomerization of the azobenzene unit, leading to tube disassembly. Thermal or photoinduced (457 nm light) recovery of the trans isomer restores the nanotubes.
CHEMICAL COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Elias J. Fernandez, Tongye Shen
Article
Physics, Multidisciplinary
Emmanuel Trizac, Tongye Shen
Article
Chemistry, Physical
Alexander K. Clark, J. Heath Wilder, Aaron W. Grayson, Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Elias J. Fernandez, Tongye Shen
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Article
Biochemistry & Molecular Biology
Quentin R. Johnson, Richard J. Lindsay, Ricky B. Nellas, Tongye Shen
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2016)
Article
Chemistry, Physical
Richard J. Lindsay, Jan Siess, David P. Lohry, Trevor S. McGee, Jordan S. Ritchie, Quentin R. Johnson, Tongye Shen
JOURNAL OF CHEMICAL PHYSICS
(2018)
Article
Chemistry, Multidisciplinary
Quentin R. Johnson, Richard J. Lindsay, Tongye Shen
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Bill Pham, Tongye Shen, Rachel Patton McCord
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Bill Pham, Richard J. Lindsay, Tongye Shen
Article
Chemistry, Medicinal
Bill Pham, Avery Bancroft Arons, Jeremy G. Vincent, Elias J. Fernandez, Tongye Shen
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2019)
Article
Biochemistry & Molecular Biology
Richard J. Lindsay, Rachael A. Mansbach, S. Gnanakaran, Tongye Shen
Summary: The conformational ensemble of intrinsically disordered proteins, such as α-synuclein, is crucial for understanding and preventing pathologies. Under low pH conditions, neutralization of negatively charged residues leads to compaction of the C-terminal portion of α-synuclein, while internal reorganization allows it to maintain its overall end-to-end distance.
BIOPHYSICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
Summary: Chromosome structures vary between different cell types and regions, and are influenced by factors such as epigenetic state.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Bill Pham, Ziju Cheng, Daniel Lopez, Richard J. Lindsay, David Foutch, Rily T. Majors, Tongye Shen
Summary: This study examines the receptor-ligand interaction patterns of the ROR gamma receptor and identifies key contacts essential to its constitutive activity. By analyzing crystal structures and performing computer simulations, the differences between agonist and inverse agonist binding are revealed. These findings have implications for the development of new drugs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
David Foutch, Bill Pham, Tongye Shen
Summary: Network analysis is a powerful tool for studying structural biology systems, with network centrality measurements and cluster coefficients helping identify key functional residues in proteins. Eigenvector centrality is sensitive in distinguishing structural features, while closeness centrality is less sensitive and more generic with respect to structural specificity. Modifications to protein structure networks (PSNs) can enhance sensitivity to discern structural changes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Priyojit Das, Tongye Shen, Rachel Patton McCord
BMC BIOINFORMATICS
(2020)
Article
Physics, Fluids & Plasmas
Priyojit Das, Rosela Golloshi, Rachel Patton McCord, Tongye Shen