macromolecular substances

Summary

Summary: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.

Top Publications

  1. Benton L, Smith A, Young G, Pielak G. Unexpected effects of macromolecular crowding on protein stability. Biochemistry. 2012;51:9773-5 pubmed publisher
    ..Furthermore, the stabilization is driven by enthalpy, not entropy. These results point to the need for carefully controlled studies and more sophisticated theories for understanding crowding effects. ..
  2. Wang Y, Sarkar M, Smith A, Krois A, Pielak G. Macromolecular crowding and protein stability. J Am Chem Soc. 2012;134:16614-8 pubmed publisher
    ..Our results show that both chemical interactions and hard-core repulsions must be considered when assessing the effects of crowding and help explain previous observations about protein stability and dynamics in cells. ..
  3. Hrabe T, Chen Y, Pfeffer S, Cuellar L, Mangold A, Förster F. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol. 2012;178:177-88 pubmed publisher
    ..PyTom enables parallelized processing of large numbers of tomograms, but also provides a convenient, sustainable environment for algorithmic development. ..
  4. Zhang L, Ren G. IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure. PLoS ONE. 2012;7:e30249 pubmed publisher
    ..Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. ..
  5. Szule J, Harlow M, Jung J, De Miguel F, Marshall R, McMahan U. Regulation of synaptic vesicle docking by different classes of macromolecules in active zone material. PLoS ONE. 2012;7:e33333 pubmed publisher
    ..Establishing the number, arrangement and sequence of association of AZM macromolecules involved in vesicle docking provides an anatomical basis for testing and extending concepts of docking mechanisms provided by biochemistry. ..
  6. Komissarov A, Florova G, Idell S. Effects of extracellular DNA on plasminogen activation and fibrinolysis. J Biol Chem. 2011;286:41949-62 pubmed publisher
    ..Conversely, DNA could inhibit fibrinolysis by increasing the susceptibility of fibrinolytic enzymes to serpins. ..
  7. Zhang D, Wu L, Chen J, Liang Y. Effects of macromolecular crowding on the structural stability of human ?-lactalbumin. Acta Biochim Biophys Sin (Shanghai). 2012;44:703-11 pubmed publisher
    ..Our data are consistent with the results of protein stability studies in cells and suggest that stabilizing excluded-volume effects of crowding agents can be ameliorated by non-specific interactions between proteins and crowders. ..
  8. Chen E, Christiansen A, Wang Q, Cheung M, Kliger D, Wittung Stafshede P. Effects of macromolecular crowding on burst phase kinetics of cytochrome c folding. Biochemistry. 2012;51:9836-45 pubmed publisher
    ..We conclude that excluded volume effects alter unfolded cytochrome c such that access to fast-folding conformations is reduced. ..
  9. Scheres S. A Bayesian view on cryo-EM structure determination. J Mol Biol. 2012;415:406-18 pubmed publisher
    ..Application to experimental data indicates that the statistical approach yields more reliable structures than existing methods and is capable of detecting smaller classes in data sets that contain multiple different structures. ..

More Information

Publications62

  1. Morelli M, Allen R, Wolde P. Effects of macromolecular crowding on genetic networks. Biophys J. 2011;101:2882-91 pubmed publisher
  2. Phillip Y, Schreiber G. Formation of protein complexes in crowded environments--from in vitro to in vivo. FEBS Lett. 2013;587:1046-52 pubmed publisher
    ..Obtaining quantitative biochemical information on reactions inside living cells is currently a main challenge of the field, as the complexity of the intracellular milieu was what motivated crowding research to begin with...
  3. Chatel Chaix L, Germain M, Motorina A, Bonneil E, Thibault P, Baril M, et al. A host YB-1 ribonucleoprotein complex is hijacked by hepatitis C virus for the control of NS3-dependent particle production. J Virol. 2013;87:11704-20 pubmed publisher
    ..Overall, our data support a model in which HCV hijacks host cell machinery containing numerous RNA-binding proteins to control the equilibrium between viral RNA replication and NS3-dependent late steps in particle production. ..
  4. Blais N, Gagné M, Hamuro Y, Rheault P, Boyer M, Steff A, et al. Characterization of Pre-F-GCN4t, a Modified Human Respiratory Syncytial Virus Fusion Protein Stabilized in a Noncleaved Prefusion Conformation. J Virol. 2017;91: pubmed publisher
    ..Our results show that Pre-F-GCN4t presents characteristics of a stabilized pre-F conformation and support its use as an RSV vaccine antigen. Such an antigen may represent a significant advance in the development of an RSV vaccine. ..
  5. Vaithianathan T, Henry D, Akmentin W, Matthews G. Nanoscale dynamics of synaptic vesicle trafficking and fusion at the presynaptic active zone. elife. 2016;5: pubmed publisher
    ..The combination of these functions allows the ribbon-type CAZ to achieve the continuous transmitter release required by synapses of neurons that carry tonic, graded visual signals in the retina. ..
  6. Hagbani T, Nazzal S. Curcumin complexation with cyclodextrins by the autoclave process: Method development and characterization of complex formation. Int J Pharm. 2017;520:173-180 pubmed publisher
    ..It was concluded that the autoclave process with its short processing time could be used as an alternate and efficient methods for drug:CD complexation. ..
  7. Song T, Keum K, Hong W. Study of nanocrystalline silicon films synthesized Below 100 degrees C by catalytic chemical vapor deposition. J Nanosci Nanotechnol. 2013;13:7519-23 pubmed
    ..By analyzing the capacitance-voltage characteristics of these diodes, we found that the hysteresis and rectifying behavior of these diodes were affected by the the nc-Si layer thickness. ..
  8. Bubeck D. The making of a macromolecular machine: assembly of the membrane attack complex. Biochemistry. 2014;53:1908-15 pubmed publisher
    ..This review highlights structural analyses of terminal pathway complexes to explore molecular mechanisms underlying MAC formation. ..
  9. Baumann J, Affolter B, von Arx U, Noel M. Alteration of urinary macromolecules by adsorption on surfaces, probably an important factor in urolithiasis. Urolithiasis. 2013;41:467-74 pubmed publisher
    ..The retardation of CaOx AGN measured in DPU could be decisive whether during crystalluria crystals are washed out from the kidney by diuresis or are attached to kidney calcifications or pre-existing stones. ..
  10. Ma J, Kelich J, Junod S, Yang W. Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex. J Cell Sci. 2017;130:1299-1306 pubmed publisher
    ..This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes. ..
  11. Booth T, Rabb M, Beniac D. How do filovirus filaments bend without breaking?. Trends Microbiol. 2013;21:583-93 pubmed publisher
    ..We review how the structure of filoviruses and paramyxoviruses permits this morphological flexibility in comparison to rhabdoviruses that have short, bullet-shaped virions with relatively rigid envelopes. ..
  12. Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Sci. 2017;: pubmed publisher
    ..4?±?0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein ?-helices...
  13. Malbet Monaco S, Leonard G, Mitchell E, Gordon E. How the ESRF helps industry and how they help the ESRF. Acta Crystallogr D Biol Crystallogr. 2013;69:1289-96 pubmed publisher
    ..This paper describes the key features of the functionality put in place on the ESRF structural biology beamlines and outlines the major advantages of the interaction of the ESRF with the pharmaceutical industry. ..
  14. Hall D. A composite polynomial approach for analyzing the indefinite self-association of macromolecules studied by sedimentation equilibrium. Biophys Chem. 2017;228:10-16 pubmed publisher
    ..The outlined method does not depend upon non-linear regression to generate a solution, but instead requires evaluation of the roots of a high-order polynomial. ..
  15. Cheng S, Brooks C. Protein-Protein Interfaces in Viral Capsids Are Structurally Unique. J Mol Biol. 2015;427:3613-3624 pubmed publisher
    ..Our finding highlights the design principle of building large biological containers from repeated, self-assembling units and provides insights into specific targets for antiviral drug design for improved efficacy. ..
  16. Lee Y, Jang S, Cho C, Bae J, Park S, Park K. Recyclable rhodium nanoparticles: green hydrothermal synthesis, characterization, and highly catalytic performance in reduction of nitroarenes. J Nanosci Nanotechnol. 2013;13:7477-81 pubmed
    ..Therefore, this method will contribute greatly to the development of environmental field and be suitable for use in the industry. ..
  17. Krojer T, Pike A, von Delft F. Squeezing the most from every crystal: the fine details of data collection. Acta Crystallogr D Biol Crystallogr. 2013;69:1303-13 pubmed publisher
    ..Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice. ..
  18. Ramsay A, Fliniaux O, Quero A, Molinie R, Demailly H, Hano C, et al. Kinetics of the incorporation of the main phenolic compounds into the lignan macromolecule during flaxseed development. Food Chem. 2017;217:1-8 pubmed publisher
    ..Secosiolariciresinol diglucoside accumulates (up to 28.65mg/g dry matter) in the later developmental stages in both forms, mainly ester-bound in the lignan macromolecule and slightly in a free form. ..
  19. Zhu Y, Ouyang Q, Mao Y. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy. BMC Bioinformatics. 2017;18:348 pubmed publisher
    ..Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing. ..
  20. Lyumkis D, Vinterbo S, Potter C, Carragher B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J Struct Biol. 2013;184:417-26 pubmed publisher
  21. Mai K, Kang M, Kang B. 3D Printing of Plant Golgi Stacks from Their Electron Tomographic Models. Methods Mol Biol. 2017;1662:105-113 pubmed publisher
    ..In this chapter, we present a simple guide to creating 3D prints of electron tomographic models of plant Golgi stacks using the two most accessible 3D printing technologies. ..
  22. Shin H, Kim E, Lee S, Lee S, Park S, Chung K, et al. Studies on formation of carborane film prepared by using a deuterium glow discharge method. J Nanosci Nanotechnol. 2013;13:7444-7 pubmed
  23. Deniz A. Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution. J Mol Biol. 2016;428:301-307 pubmed publisher
    ..Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects. ..
  24. Sigworth F. Principles of cryo-EM single-particle image processing. Microscopy (Oxf). 2016;65:57-67 pubmed publisher
    ..Also considered are the limits that image signal-to-noise ratio places on resolution and the distinguishing of heterogeneous particle populations. ..
  25. Hong U, Park H, Lee J, Hwang S, Kwak J, Yi J, et al. Hydrogenation of succinic acid to 1,4-butanediol over rhenium catalyst supported on copper-containing mesoporous carbon. J Nanosci Nanotechnol. 2013;13:7448-53 pubmed
    ..Fine dispersion of copper in the Re/Cu-MC catalyst was responsible for its enhanced catalytic activity. ..
  26. Liu B, Li W, Zhao J, Liu Y, Zhu X, Liang G. Physicochemical characterisation of the supramolecular structure of luteolin/cyclodextrin inclusion complex. Food Chem. 2013;141:900-6 pubmed publisher
    ..Furthermore, molecular docking study showed that the complex was formed with the B ring of luteolin inserted into the cavity of G-?-CD. ..
  27. Ahvaz H, Mobasheri H, Bakhshandeh B, Shakhssalim N, Naji M, Dodel M, et al. Mechanical characteristics of electrospun aligned PCL/PLLA nanofibrous scaffolds conduct cell differentiation in human bladder tissue engineering. J Nanosci Nanotechnol. 2013;13:4736-43 pubmed
    ..We found that mechanical forces with different frequencies exert different regulatory effects on extracellular matrices and contractile genes in hBSMCs and hBUCs that should be considered in tissue engineering strategies. ..
  28. Rhee S, Rusch N. Molecular determinants of beta-adrenergic signaling to voltage-gated K+ channels in the cerebral circulation. Microcirculation. 2018;25: pubmed publisher
  29. Johansson L, Stauch B, Ishchenko A, Cherezov V. A Bright Future for Serial Femtosecond Crystallography with XFELs. Trends Biochem Sci. 2017;42:749-762 pubmed publisher
  30. Zeng C, Xin R, Qi S, Yang B, Wang Y. Aqueous two-phase system based on natural quaternary ammonium compounds for the extraction of proteins. J Sep Sci. 2016;39:648-54 pubmed publisher
  31. Kim M, Kim D, Kim S, Leem J. Structural and optical properties of ZnO nanorods on Mg0.2Zn0.8O seed layers grown by hydrothermal method. J Nanosci Nanotechnol. 2013;13:3408-12 pubmed
    ..2Zn0.8O seed layers with 5 layers (thickness of 350 nm), which indicate the enhancement the structural and the optical properties of the ZnO nanorods. ..
  32. Hiraishi N, Ishida Y, Nagahama M. AAA-ATPase NVL2 acts on MTR4-exosome complex to dissociate the nucleolar protein WDR74. Biochem Biophys Res Commun. 2015;467:534-40 pubmed publisher
    ..Knockdown of WDR74 decreases 60S ribosome levels. Taken together, our results suggest that WDR74 is a novel regulatory protein of the MTR4-exsosome complex whose interaction is regulated by NVL2 and is involved in ribosome biogenesis. ..
  33. Höst G, Larsson C, Olson A, Tibell L. Student learning about biomolecular self-assembly using two different external representations. CBE Life Sci Educ. 2013;12:471-82 pubmed publisher
    ..A tentative difference was observed in response complexity, with more multifaceted responses in the tangible model condition. ..
  34. Karnabi E, Qu Y, Yue Y, Boutjdir M. Calreticulin negatively regulates the surface expression of Cav1.3 L-type calcium channel. Biochem Biophys Res Commun. 2013;437:497-501 pubmed publisher
    ..The data demonstrate a novel mechanism of modulation of Cav1.3 Ca channel by calreticulin, which may be involved in pathological settings such as autoimmune associated congenital heart block where Cav1.3 Ca channels are downregulated. ..
  35. Qian Q, Huang X, Zhang X, Xie Z, Wang Y. One-step preparation of macroporous polymer particles with multiple interconnected chambers: a candidate for trapping biomacromolecules. Angew Chem Int Ed Engl. 2013;52:10625-9 pubmed publisher
    ..These particles can act as smart containers to encapsulate and hold DNA molecules. ..
  36. Johnstone T, Kulak N, Pridgen E, Farokhzad O, Langer R, Lippard S. Nanoparticle encapsulation of mitaplatin and the effect thereof on in vivo properties. ACS Nano. 2013;7:5675-83 pubmed publisher
  37. Turoňová B, Schur F, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. J Struct Biol. 2017;199:187-195 pubmed publisher
    ..We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4Å resolution structure determined by subtomogram averaging. ..
  38. Chalikian T. Excluded volume contribution to cosolvent-mediated modulation of macromolecular folding and binding reactions. Biophys Chem. 2016;209:1-8 pubmed publisher
    ..This notion has implications for understanding the long-standing observation that, in osmotic stress studies, various osmolytes may produce significantly distinct estimates of hydration/dehydration for the same reaction. ..
  39. Sun X, Zhang J, Wang X, Zhang C, Hu P, Mu Y, et al. Oligothiophenes on CVD graphene grown on multi-crystalline copper foil: supramolecular assembly and impact of morphology. Chem Commun (Camb). 2013;49:10317-9 pubmed publisher
    ..Most importantly, we found that the graphene ripple structures, even with a height as small as ~0.5 nm, can significantly alter the molecule-substrate interaction, which has never been observed previously. ..
  40. Sarkar M, Smith A, Pielak G. Impact of reconstituted cytosol on protein stability. Proc Natl Acad Sci U S A. 2013;110:19342-7 pubmed publisher
    ..The effects of the cytosol are even stronger than those of homogeneous protein crowders, reinforcing the biological significance of weak, nonspecific interactions. ..
  41. Feng L, Yang J, Zhao J, Wang D, Koynov K, Butt H. Fluorescence correlation spectroscopy of repulsive systems: theory, simulation, and experiment. J Chem Phys. 2013;138:214902 pubmed publisher
    ..These theoretical results are successfully proven using Brownian dynamics simulations and preliminary FCS experiments for model charged colloidal systems. ..
  42. Yu G, Li K, Jiang W. Antibody-based affinity cryo-EM grid. Methods. 2016;100:16-24 pubmed publisher
  43. Yi J, Khobrekar N, Dantas T, Zhou J, Vallee R. Imaging of motor-dependent transport in neuronal and nonneuronal cells at high spatial and temporal resolution. Methods Cell Biol. 2016;131:453-65 pubmed publisher
    ..We discuss long-term inhibition, as well as short-term inhibition methods when needed to minimize complications from motor protein interactions. ..
  44. Luján R, Aguado C. Localization and Targeting of GIRK Channels in Mammalian Central Neurons. Int Rev Neurobiol. 2015;123:161-200 pubmed publisher
    ..Here, we present an overview of studies aimed at determining the cellular and subcellular localization of GIRK channel subunits in mammalian brain neurons and discuss implications for neuronal physiology. ..
  45. Chan J, Lewis D, Petersen L, Moghe P, Uhrich K. Amphiphilic macromolecule nanoassemblies suppress smooth muscle cell proliferation and platelet adhesion. Biomaterials. 2016;84:219-229 pubmed publisher
    ..Thus, AM micelles and NPs can effectively repress early stage SMC proliferation and thrombosis through non-cytotoxic mechanisms, highlighting the promise of nanomedicine for next-generation cardiovascular therapeutics. ..
  46. Mutter F, Park B, Copple I. Value of monitoring Nrf2 activity for the detection of chemical and oxidative stress. Biochem Soc Trans. 2015;43:657-62 pubmed publisher
    ..We also provide an outlook on the potential value of monitoring Nrf2 activity for improving the pre-clinical identification of chemicals and drugs with toxic liability in humans. ..
  47. Bosse J, Hogue I, Feric M, Thiberge S, Sodeik B, Brangwynne C, et al. Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion. Proc Natl Acad Sci U S A. 2015;112:E5725-33 pubmed publisher
    ..Instead, infection with different herpesviruses induced an enlargement of interchromatin domains and allowed particles to diffuse unrestricted over longer distances, thereby facilitating nuclear egress for a larger fraction of capsids. ..
  48. Thierry A, El Messaoudi S, Gahan P, Anker P, Stroun M. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev. 2016;35:347-76 pubmed publisher
    ..A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects. ..
  49. Pulido Companys A, Albalat R, Garcia Amorós J, Velasco D, Ignés Mullol J. Supramolecular organization and heterochiral recognition in Langmuir monolayers of chiral azobenzene surfactants. Langmuir. 2013;29:9635-42 pubmed publisher
  50. Kuan S, Ng D, Wu Y, Förtsch C, Barth H, Doroshenko M, et al. pH responsive Janus-like supramolecular fusion proteins for functional protein delivery. J Am Chem Soc. 2013;135:17254-7 pubmed publisher
  51. Kim S, Kim J, Choe J, Byun Y, Seo J, Kim D. Fabrication of electrically conductive nickel-silver bimetallic particles via polydopamine coating. J Nanosci Nanotechnol. 2013;13:7600-9 pubmed
    ..XRD patterns also confirmed the presence of Ag in a metallic state. In addition, the sheet resistance of as-prepared composite particles showed a tendency to decrease with increasing AgNO3 concentration. ..
  52. Briddon S, Kilpatrick L, Hill S. Studying GPCR Pharmacology in Membrane Microdomains: Fluorescence Correlation Spectroscopy Comes of Age. Trends Pharmacol Sci. 2018;39:158-174 pubmed publisher
    ..Once the preserve of specialist equipment, FCS techniques can now be applied using standard confocal microscopes. This review describes how FCS and related techniques have revealed novel insights into GPCR biology. ..
  53. Smirnova E, Safenkova I, Stein Margolina B, Shubin V, Gurvits B. L-arginine induces protein aggregation and transformation of supramolecular structures of the aggregates. Amino Acids. 2013;45:845-55 pubmed publisher
    ..The interaction of another positively charged amino acid L-lysine with ?-lactalbumin also resulted in profound acceleration of the aggregation process and transformation of supramolecular structures of the aggregates. ..