Monitoring the GAP catalyzed H-Ras GTPase reaction at atomic resolution in real time

The molecular reaction mechanism of the GTPase-activating protein (GAP)-catalyzed GTP hydrolysis by Ras was investigated by time resolved Fourier transform infrared (FTIR) difference spectroscopy using caged GTP (P3-1-(2-nitro)phenylethyl guanosine 5′-O-triphosphate) as photolabile trigger. This approach provides the complete GTPase reaction pathway with time resolution of milliseconds at the atomic level. Up to now, one structural model of the GAP⋅Ras⋅GDP⋅AlFx transition state analog is known, which represents a “snap shot” along the reaction-pathway. As now revealed, binding of GAP to Ras⋅GTP shifts negative charge from the γ to β phosphate. Such a shift was already identified by FTIR in GTP because of Ras binding and is now shown to be enhanced by GAP binding. Because the charge distribution of the GAP⋅Ras⋅GTP complex thus resembles a more dissociative-like transition state and is more like that in GDP, the activation free energy is reduced. An intermediate is observed on the reaction pathway that appears when the bond between β and γ phosphate is cleaved. In the intermediate, the released Pi is strongly bound to the protein and surprisingly shows bands typical of those seen for phosphorylated enzyme intermediates. All these results provide a mechanistic picture that is different from the intrinsic GTPase reaction of Ras. FTIR analysis reveals the release of Pi from the protein complex as the rate-limiting step for the GAP-catalyzed reaction. The approach presented allows the study not only of single proteins but of protein–protein interactions without intrinsic chromophores, in the non-crystalline state, in real time at the atomic level.

Direct atomic force microscope imaging of EcoRI endonuclease site specifically bound to plasmid DNA molecules.

Direct imaging with the atomic force microscope has been used to identify specific nucleotide sequences in plasmid DNA molecules. This was accomplished using EcoRI (Gln-111), a mutant of the restriction enzyme that has a 1000-fold greater binding affinity than the wild-type enzyme but with cleavage rate constants reduced by a factor of 10(4). ScaI-linearized plasmids with single (pBS+) and double (pGEM-luc and pSV-beta-galactosidase) EcoRI recognition sites were imaged, and the bound enzyme was localized to a 50- to 100-nt resolution. The high affinity for the EcoRI binding site exhibited by this mutant endonuclease, coupled with an observed low level of nonspecific binding, should prove valuable for physically mapping large DNA clones by direct atomic force microscope imaging.

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxin-encoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H...S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(Scys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.

Imaging ROMK1 inwardly rectifying ATP-sensitive K+ channel protein using atomic force microscopy.

The inwardly rectifying K+ channel ROMK1 has been implicated as being significant in K+ secretion in the distal nephron. ROMK1 has been shown by immunocytochemistry to be expressed in relevant nephron segments. The development of the atomic force microscope has made possible the production of high resolution images of small particles, including a variety of biological macromolecules. Recently, a fusion protein of glutathione S-transferase (GST) and ROMK1 (ROMK1-GST) has been used to produce a polyclonal antibody for immunolocalization of ROMK1. We have used atomic force microscopy to examine ROMK1-GST and the native ROMK1 polypeptide cleaved from GST. Imaging was conducted with the proteins in physiological solutions attached to mica. ROMK1-GST appears in images as a particle composed of two units of similar size. Analyses of images indicate that the two units have volumes of approximately 118 nm3, which is close to the theoretical volume of a globular protein of approximately 65 kDa (the molecular mass of ROMK1-GST). Native GST exists as a dimer, and the images obtained here are consistent with the ROMK1-GST fusion protein's existence as a heterodimer. In experiments on ROMK1 in aqueous solution, single molecules appear to aggregate, but contact to the mica was maintained. Addition of ATP to the solution produced a change in height of the aggregates. This change (which was reversible) suggests that ATP induces a structural change in the ROMK1 protein. The data show that atomic force microscopy is a useful tool for examination of purified protein molecules under near-physiological conditions, and furthermore, that structural alterations in the proteins may be continuously investigated.

Detection and localization of individual antibody-antigen recognition events by atomic force microscopy.

A methodology has been developed for the study of molecular recognition at the level of single events and for the localization of sites on biosurfaces, in combining force microscopy with molecular recognition by specific ligands. For this goal, a sensor was designed by covalently linking an antibody (anti-human serum albumin, polyclonal) via a flexible spacer to the tip of a force microscope. This sensor permitted detection of single antibody-antigen recognition events by force signals of unique shape with an unbinding force of 244 +/- 22 pN. Analysis revealed that observed unbinding forces originate from the dissociation of individual Fab fragments from a human serum albumin molecule. The two Fab fragments of the antibody were found to bind independently and with equal probability. The flexible linkage provided the antibody with a 6-nm dynamical reach for binding, rendering binding probability high, 0.5 for encounter times of 60 ms. This permitted fast and reliable detection of antigenic sites during lateral scans with a positional accuracy of 1.5 nm. It is indicated that this methodology has promise for characterizing rate constants and kinetics of molecular recognition complexes and for molecular mapping of biosurfaces such as membranes.

Direct measurement of hydrogen bonding in DNA nucleotide bases by atomic force microscopy.

We have used self-assembled purines and pyrimidines on planar gold surfaces and on gold-coated atomic force microscope (AFM) tips to directly probe intermolecular hydrogen bonds. Electron spectroscopy for chemical analysis (ESCA) and thermal programmed desorption (TPD) measurements of the molecular layers suggested monolayer coverage and a desorption energy of about 25 kcal/mol. Experiments were performed under water, with all four DNA bases immobilized on AFM tips and flat surfaces. Directional hydrogen-bonding interaction between the tip molecules and the surface molecules could be measured only when opposite base-pair coatings were used. The directional interactions were inhibited by excess nucleotide base in solution. Nondirectional van der Waals forces were present in all other cases. Forces as low as two interacting base pairs have been measured. With coated AFM tips, surface chemistry-sensitive recognition atomic force microscopy can be performed.

Characterizations of logarithmic Besov spaces in terms of differences, Fourier-analytical decompositions, wavelets and semi-groups.

We work with Besov spaces Bp,q0,b defined by means of differences, with zero classical smoothness and logarithmic smoothness with exponent b. We characterize Bp,q0,b by means of Fourier-analytical decompositions, wavelets and semi-groups. We also compare those results with the well-known characterizations for classical Besov spaces Bp,qs.

Kinetic study of the decompositions involved in the thermal degradation of commercial azodicarbonamide

The transitions and reactions involved in the thermal treatment of several commercial azodicarbonamides (ADC) in an inert atmosphere have been studied by dynamic thermogravimetry analysis (TGA), mass spectrometry and Fourier transform infrared (FTIR) spectroscopy. A pseudo-mechanistic model, involving several competitive and non-competitive reactions, has been suggested and applied to the correlation of the weight loss data. The model applied is capable of accurately representing the different processes involved, and can be of great interest in the understanding and quantification of such phenomena, including the simulation of the instantaneous amount of gases evolved in a foaming process. In addition, a brief discussion on the methodology related to the mathematical modeling of TGA data is presented, taking into account the complex thermal behaviour of the ADC.

Quantum interference in atomic-sized point contacts

The conductance of atomic-sized metallic point contacts is shown to be strongly voltage dependent due to quantum interference with impurities even in samples with low impurity concentrations. Transmission through these small contacts depends not only on the local atomic structure at the contact but also on the distribution of impurities or defects within a coherence length of the contact. In contrast with other mesoscopic systems we show that transport through atomic contacts is coherent even at room temperature. The use of a scanning tunneling microscope (STM) makes it possible to fabricate one atom contacts of gold whose transmission can be controlled by manipulation of the contact allowing inelastic spectroscopy in such small contacts.

Absence of magnetically induced fractional quantization in atomic contacts

Using the mechanically controlled break junction technique at low temperatures and under cryogenic vacuum conditions we have studied atomic contacts of several magnetic (Fe, Co, and Ni) and nonmagnetic (Pt) metals, which recently were claimed to show fractional conductance quantization. In the case of pure metals we see no quantization of the conductance nor half quantization, even when high magnetic fields are applied. On the other hand, features in the conductance similar to (fractional) quantization are observed when the contact is exposed to gas molecules. Furthermore, the absence of fractional quantization when the contact is bridged by H2 indicates the current is never fully polarized for the metals studied here. Our results are in agreement with recent model calculations.

Analysis of the Kondo effect in ferromagnetic atomic-sized contacts

Atomic contacts made of ferromagnetic metals present zero-bias anomalies in the differential conductance due to the Kondo effect. These systems provide a unique opportunity to perform a statistical analysis of the Kondo parameters in nanostructures since a large number of contacts can be easily fabricated using break-junction techniques. The details of the atomic structure differ from one contact to another so a large number of different configurations can be statistically analyzed. Here we present such a statistical analysis of the Kondo effect in atomic contacts made from the ferromagnetic transition metals Ni, Co, and Fe. Our analysis shows clear differences between materials that can be understood by fundamental theoretical considerations. This combination of experiments and theory allows us to extract information about the origin and nature of the Kondo effect in these systems and to explore the influence of geometry and valence in the Kondo screening of atomic-sized nanostructures.

Evolution of conducting channels in metallic atomic contacts under elastic deformation

We investigate both experimentally and theoretically the evolution of conductance in metallic one-atom contacts under elastic deformation. While simple metals like Au exhibit almost constant conductance plateaus, Al and Pb show inclined plateaus with positive and negative slopes. It is shown how these behaviors can be understood in terms of the orbital structure of the atoms forming the contact. This analysis provides further insight into the issue of conductance quantization in metallic contacts revealing important aspects of their atomic and electronic structures.

Onset of energy dissipation in ballistic atomic wires

Electronic transport at finite voltages in free-standing gold atomic chains of up to seven atoms in length is studied at low temperatures using a scanning tunneling microscope. The conductance vs voltage curves show that transport in these single-mode ballistic atomic wires is nondissipative up to a finite voltage threshold of the order of several mV. The onset of dissipation and resistance within the wire corresponds to the excitation of the atomic vibrations by the electrons traversing the wire and is very sensitive to strain.