Article
Biochemistry & Molecular Biology
Sarah Dallo, Jeehae Shin, Shanwen Zhang, Qian Ren, Huan Bao
Summary: Signal transduction at the synapse relies on protein-lipid interactions for the regulation of synaptic vesicle biogenesis, neurotransmitter release, and postsynaptic receptor activation. Recent advances in nanodiscs have greatly enhanced our ability to study and manipulate these interactions, offering new opportunities for understanding synaptic transmission.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lauren E. Ball, Liam J. Riley, Waled Hadasha, Rueben Pfukwa, Corinne J. Smith, Timothy R. Dafforn, Bert Klumperman
Summary: Polymer-based lipid nanoparticles, such as DIBMA, have shown significant advancements in the study of membrane proteins. Research indicates that DIBMA exhibits excellent performance in lipid nanodisc formation and membrane protein extraction, with better solubilization efficiency and cleaner separation compared to SMA and commercially available DIBMA.
Review
Biochemistry & Molecular Biology
Stephen G. Sligar, Ilia G. Denisov
Summary: Membrane proteins play crucial roles in biological processes, but are often challenging to study. The NanoDisc platform offers a self-assembled system that solubilizes membrane proteins in water while maintaining their functional activity. NanoDiscs have utility in studying cellular signaling complexes and delivering drugs, showcasing their versatility in biochemistry and pharmacology.
Article
Biochemistry & Molecular Biology
Madhumalar Subramanian, Charlotte Kielar, Satoru Tsushima, Karim Fahmy, Jana Oertel
Summary: The use of engineered cysteines on membrane-scaffolding protein MSP1D1 allows the formation of multimers of nanodiscs, which is crucial for membrane protein research. Minimal interference with nanodisc formation and structure was demonstrated by various analytical techniques. Transmission electron microscopy showed the growth of submicron-sized tracts of stacked nanodiscs through oligonucleotide attachment to engineered cysteines.
Article
Biochemistry & Molecular Biology
Irfan Prabudiansyah, Ramon van der Valk, Marie-Eve Aubin-Tam
Summary: FtsH is a membrane-bound protease that plays a crucial role in regulating cellular functions, and can maintain its activity when reconstituted into lipid nanodiscs. Research has shown that the lipid bilayer composition affects the proteolytic activity of FtsH.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Biochemistry & Molecular Biology
Shweta Shree, Mark A. McLean, Andrew G. Stephen, Stephen G. Sligar
Summary: KRas4b is a membrane-bound regulatory protein involved in signal transduction and cell growth, and its conformation is influenced by anionic lipids.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Bankala Krishnarjuna, Ayyalusamy Ramamoorthy
Summary: Atomic-resolution structural studies of membrane-associated proteins and peptides in a membrane environment are important for understanding their biological function and disease pathology. Recent advancements in NMR spectroscopy, cryoEM approaches, and the development of novel membrane mimetics have overcome the complexity of the cell membrane and enabled reconstitution and investigation of membrane proteins.
Article
Chemistry, Multidisciplinary
Kin Kuan Hoi, Juan Francisco Bada Juarez, Peter J. Judge, Hsin-Yung Yen, Di Wu, Javier Vinals, Garrick F. Taylor, Anthony Watts, Carol Robinson
Summary: The study used native MS to investigate the spectra of membrane proteins in different membrane mimetics, revealing that SMA may favor selective solubilization of correctly folded proteins. The results provide insights into the correlation between PTMs, lipid interactions, and protein folding states.
Article
Biochemistry & Molecular Biology
D. S. Molodenskiy, D. Svergun, H. D. T. Mertens
Summary: Membrane proteins are important targets in biological and medical sciences, and small-angle X-ray scattering provides a rapid method for studying their structures and conformational changes. MPBuilder is a versatile tool that allows for generating and refining membrane protein systems in the popular PyMOL software.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Justin Amengual, Luke Notaro-Roberts, Mu -Ping Nieh
Summary: Bicellar systems have gained popularity in the fields of biochemistry, physical chemistry, and drug delivery technology due to their diverse morphology. They have been used as model membranes for studying transmembrane protein behavior and interactions with the cell. Additionally, they have shown potential as theranostic nanocarriers in biopharmaceutical and diagnostic research.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Nicolai Tidemand Johansen, Frederik Gronbaek Tidemand, Martin Cramer Pedersen, Lise Arleth
Summary: We have witnessed significant progress in the design, optimization, and utilization of carrier particle systems for studying membrane proteins in near-native environments over the past decade. New and improved systems continue to emerge, pushing the boundaries of existing carrier systems, while specific carrier systems establish themselves as the preferred choice for certain types of target membrane proteins. This review covers the most commonly used carrier systems, highlighting their similarities and differences, as well as current trends and future directions in the field. Special attention is given to the biophysical properties and membrane mimicking ability of each system, and how they may impact the study of embedded membrane proteins and their structure or function.
Article
Chemistry, Multidisciplinary
Tao Chen, Feng Pan, Gan Luo, Kuan Jiang, Huan Wang, Tianhao Ding, Wei Li, Changyou Zhan, Xiaoli Wei
Summary: PEGylated lipid-based nanocarriers have improved drug delivery efficiency while reducing toxicity. Protein corona formation alters their biological identity and affects their in vivo performance. This study discovered that discoid-shaped lipid nanodiscs have a unique protein corona pattern, reducing complement binding and activation, avoiding accelerated blood clearance, and exhibiting brain targeting capability.
Article
Biochemistry & Molecular Biology
Lorela Paco, John C. Hackett, William M. Atkins
Summary: Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of various drugs and toxins. The interactions between CYP3A4 and ligands are difficult to predict due to its promiscuity and conformational flexibility. Through the use of hydrogen deuterium exchange mass spectrometry (HDX-MS), we investigated the effect of ligands on nanodisc-embedded CYP3A4, and found that ligands have differential effects on the flexibility of different regions of the enzyme. Molecular dynamics simulations showed that ligands can modulate long-range interactions and propagate local backbone fluctuations from the binding site to flexible regions of CYP3A4. Contrary to the common paradigm, a wide range of ligands actually increase the overall dynamics of CYP3A4, including regions remote from the active site.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Johannes Thoma, Bjorn M. Burmann
Summary: Membrane proteins are evolved to reside in the hydrophobic lipid bilayers of cellular membranes, bridging different aqueous compartments separated by the membrane and dynamically interacting with their surrounding lipid environment. This interaction not only stabilizes membrane proteins, but also influences their folding, structure, and function.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Materials Science, Multidisciplinary
Orion Shih, Yi-Qi Yeh, Kuei-Fen Liao, Kun-Mou Li, Jia-Yin Tsai, Chieh-Chin Li, Yun-Wei Chiang, Richard K. Heenan, Yuh-Ju Sun, U-Ser Jeng
Summary: This study reveals the conformations and compositions of a proton-translocating pyrophosphatase Vigna radiata H+-PPase (VrPPase) in either detergent molecules or lipid nanodisc using SEC-SAXS, providing a deeper understanding of membrane-protein complexes.
MATERIALS CHEMISTRY AND PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Murugappan Sathappa, Nathan N. Alder
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2016)
Article
Chemistry, Multidisciplinary
Kevin J. Boyd, Nathan N. Alder, Eric R. May
Article
Multidisciplinary Sciences
Ketan Malhotra, Arnab Modak, Shivangi Nangia, Tyler H. Daman, Umut Gunsel, Victoria L. Robinson, Dejana Mokranjac, Eric R. May, Nathan N. Alder
Article
Biophysics
Kevin J. Boyd, Nathan N. Alder, Eric R. May
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Lijun Liu, Tarjani M. Thaker, Daniel M. Freed, Nicole Frazier, Ketan Malhotra, Mark A. Lemmon, Natalia Jura
Article
Gastroenterology & Hepatology
Kang Kwang Lee, Naoki Imaizumi, Sally R. Chamberland, Nathan N. Alder, Urs A. Boelsterli
Article
Multidisciplinary Sciences
Elizabeth Calzada, Erica Avery, Pingdewinde N. Sam, Arnab Modak, Chunyan Wang, J. Michael McCaffery, Xianlin Han, Nathan N. Alder, Steven M. Claypool
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Minkyung Bae, Yoojin Lee, Young-Ki Park, Dong-Guk Shin, Pujan Joshi, Seung-Hyun Hong, Nathan Alder, Sung I. Koo, Ji-Young Lee
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Wayne Mitchell, Emily A. Ng, Jeffrey D. Tamucci, Kevin J. Boyd, Murugappan Sathappa, Adrian Coscia, Meixia Pan, Xianlin Han, Nicholas A. Eddy, Eric R. May, Hazel H. Szeto, Nathan N. Alder
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Joshua B. Sheetz, Sebastian Mathea, Hanna Karvonen, Ketan Malhotra, Deep Chatterjee, Wilhelmiina Niininen, Robert Perttila, Franziska Preuss, Krishna Suresh, Steven E. Stayrook, Yuko Tsutsui, Ravi Radhakrishnan, Daniela Ungureanu, Stefan Knapp, Mark A. Lemmon
Review
Biochemistry & Molecular Biology
Joseph C. Iovine, Steven M. Claypool, Nathan N. Alder
Summary: Compartmentalization within cellular structures refers to the spatial segregation of macromolecules, metabolites, and biochemical pathways, bridging organellar structure and function. Mitochondria, with their morphological complexity and dynamic polymorphism, undergo morphogenesis events that must be considered both spatially and temporally. Disturbance in mitochondrial compartmentalization can lead to dysfunction associated with heritable and aging-related diseases.
TRENDS IN BIOCHEMICAL SCIENCES
(2021)
Article
Biology
Wayne Mitchell, Jeffrey D. Tamucci, Emery L. Ng, Shaoyi Liu, Alexander Birk, Hazel H. Szeto, Eric R. May, Andrei T. Alexandrescu, Nathan N. Alder
Summary: Mitochondria play a key role in metabolic homeostasis and their dysfunction is associated with various diseases. This study analyzed the structure-activity relationship of tetrapeptide analogs with different aromatic side chain compositions and sequence registrations. The results showed that these analogs adopt compact reverse turn conformations when bound to membranes and exhibit differences in membrane interactions. The analogs had effects on membrane surface charge and were able to penetrate cells and target mitochondria without strict requirements for side chain composition or sequence register. The analog with tryptophan side chains showed the strongest impact on membrane properties and had the highest efficacy in cell culture studies.