Structural information, resolution, and noise in high-resolution atomic force microscopy topographs.

AFM has developed into a powerful tool in structural biology, providing topographs of proteins under close-to-native conditions and featuring an outstanding signal/noise ratio. However, the imaging mechanism exhibits particularities: fast and slow scan axis represent two independent image acquisition axes. Additionally, unknown tip geometry and tip-sample interaction render the contrast transfer function nondefinable. Hence, the interpretation of AFM topographs remained difficult. How can noise and distortions present in AFM images be quantified? How does the number of molecule topographs merged influence the structural information provided by averages? What is the resolution of topographs? Here, we find that in high-resolution AFM topographs, many molecule images are only slightly disturbed by noise, distortions, and tip-sample interactions. To identify these high-quality particles, we propose a selection criterion based on the internal symmetry of the imaged protein. We introduce a novel feature-based resolution analysis and show that AFM topographs of different proteins contain structural information beginning at different resolution thresholds: 10 A (AqpZ), 12 A (AQP0), 13 A (AQP2), and 20 A (light-harvesting-complex-2). Importantly, we highlight that the best single-molecule images are more accurate molecular representations than ensemble averages, because averaging downsizes the z-dimension and "blurs" structural details.

[1]  H Luecke,et al.  Structure of bacteriorhodopsin at 1.55 A resolution. , 1999, Journal of molecular biology.

[2]  M Unser,et al.  The spectral signal-to-noise ratio resolution criterion: computational efficiency and statistical precision. , 1989, Ultramicroscopy.

[3]  A. Engel.  Microscopic assessment of membrane protein structure and function , 2003, Histochemistry and Cell Biology.

[4]  Robert M Stroud,et al.  The channel architecture of aquaporin 0 at a 2.2-A resolution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[5]  M. Rossmann,et al.  The structure of an insect parvovirus (Galleria mellonella densovirus) at 3.7 A resolution. , 1998, Structure.

[6]  G Büldt,et al.  Imaging purple membranes in aqueous solutions at sub-nanometer resolution by atomic force microscopy. , 1995, Biophysical journal.

[7]  Ws. Rasband.  ImageJ, U.S. National Institutes of Health, Bethesda, Maryland, USA , 2011 .

[8]  Sergio Marco,et al.  Nanodissection and high-resolution imaging of the Rhodopseudomonas viridis photosynthetic core complex in native membranes by AFM , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Henning Stahlberg,et al.  The 4.5 A structure of human AQP2. , 2005, Journal of molecular biology.

[10]  T. Walz,et al.  Structural models of the supramolecular organization of AQP0 and connexons in junctional microdomains. , 2007, Journal of structural biology.

[11]  J Frank,et al.  Computer averaging of electron micrographs of 40S ribosomal subunits. , 1981, Science.

[12]  R. Henderson,et al.  Molecular structure determination by electron microscopy of unstained crystalline specimens. , 1975, Journal of molecular biology.

[13]  M. Unser,et al.  A new resolution criterion based on spectral signal-to-noise ratios. , 1987, Ultramicroscopy.

[14]  Peter Agre,et al.  Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Akinori Kidera,et al.  Surface of bacteriorhodopsin revealed by high-resolution electron crystallography , 1997, Nature.

[16]  Joachim Frank,et al.  Electron microscopy of functional ribosome complexes. , 2003, Biopolymers.

[17]  S. Scheuring,et al.  High‐resolution AFM topographs of Rubrivivax gelatinosus light‐harvesting complex LH2 , 2001, The EMBO journal.

[18]  Simon Scheuring,et al.  Variable LH2 stoichiometry and core clustering in native membranes of Rhodospirillum photometricum , 2004, The EMBO journal.

[19]  A. Engel,et al.  Surface tongue-and-groove contours on lens MIP facilitate cell-to-cell adherence. , 2000, Journal of molecular biology.

[20]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[21]  A. Engel,et al.  High-resolution imaging of bacteriorhodopsin by atomic force microscopy. , 2004, Methods in molecular biology.

[22]  S. Scheuring,et al.  AFM characterization of tilt and intrinsic flexibility of Rhodobacter sphaeroides light harvesting complex 2 (LH2). , 2003, Journal of molecular biology.

[23]  R. Henderson,et al.  Three-dimensional model of purple membrane obtained by electron microscopy , 1975, Nature.

[24]  W. Kühlbrandt,et al.  Mechanisms of photoprotection and nonphotochemical quenching in pea light‐harvesting complex at 2.5 Å resolution , 2005, The EMBO journal.

[25]  A. Engel,et al.  Two‐dimensional crystals: a powerful approach to assess structure, function and dynamics of membrane proteins , 2001, FEBS letters.

[26]  S. Lowen.  The Biophysical Journal , 1960, Nature.

[27]  Robert M Stroud,et al.  Architecture and Selectivity in Aquaporins: 2.5 Å X-Ray Structure of Aquaporin Z , 2003, PLoS biology.

[28]  Simon Scheuring,et al.  Chromatic Adaptation of Photosynthetic Membranes , 2005, Science.

[29]  M. Borgnia,et al.  Structure of the water channel AqpZ from Escherichia coli revealed by electron crystallography. , 1999, Journal of molecular biology.

[30]  W. Faigle,et al.  Human cataract lens membrane at subnanometer resolution. , 2007, Journal of molecular biology.

[31]  A. Engel,et al.  Mapping flexible protein domains at subnanometer resolution with the atomic force microscope , 1998, FEBS letters.

[32]  Thomas Boudier,et al.  From high-resolution AFM topographs to atomic models of supramolecular assemblies. , 2007, Journal of structural biology.

[33]  Henning Stahlberg,et al.  Structural biology: Proton-powered turbine of a plant motor , 2000, Nature.

[34]  Gerber,et al.  Atomic Force Microscope , 2020, Definitions.

[35]  A. Engel,et al.  Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy. , 1995, Science.

[36]  M. Borgnia,et al.  High resolution AFM topographs of the Escherichia coli water channel aquaporin Z , 1999, The EMBO journal.

[37]  W. O. Saxton,et al.  The correlation averaging of a regularly arranged bacterial cell envelope protein , 1982, Journal of microscopy.

[38]  Thomas Walz,et al.  The supramolecular architecture of junctional microdomains in native lens membranes , 2007, EMBO reports.

[39]  D. Vestweber,et al.  Molecular mechanisms that control leukocyte extravasation: the selectins and the chemokines. , 1999, Histochemistry and cell biology.

[40]  S. Scheuring,et al.  Malformation of junctional microdomains in cataract lens membranes from a type II diabetes patient , 2009, Pflügers Archiv - European Journal of Physiology.

[41]  S. Harrison,et al.  Lipid–protein interactions in double-layered two-dimensional AQP0 crystals , 2005, Nature.

[42]  A. Engel,et al.  Atomic-force microscopy: Rhodopsin dimers in native disc membranes , 2003, Nature.

[43]  S. Grzesiek,et al.  Direct observation of Calpha-Halpha...O=C hydrogen bonds in proteins by interresidue h3JCalphaC' scalar couplings. , 2003, Journal of the American Chemical Society.