Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates

Point mutants of three unrelated antifluorescein antibodies were constructed to obtain nine different single-chain Fv fragments, whose on-rates, off-rates, and equilibrium binding affinities were determined in solution. Additionally, activation energies for unbinding were estimated from the temperature dependence of the off-rate in solution. Loading rate-dependent unbinding forces were determined for single molecules by atomic force microscopy, which extrapolated at zero force to a value close to the off-rate measured in solution, without any indication for multiple transition states. The measured unbinding forces of all nine mutants correlated well with the off-rate in solution, but not with the temperature dependence of the reaction, indicating that the same transition state must be crossed in spontaneous and forced unbinding and that the unbinding path under load cannot be too different from the one at zero force. The distance of the transition state from the ground state along the unbinding pathway is directly proportional to the barrier height, regardless of the details of the binding site, which most likely reflects the elasticity of the protein in the unbinding process. Atomic force microscopy thus can be a valuable tool for the characterization of solution properties of protein-ligand systems at the single molecule level, predicting relative off-rates, potentially of great value for combinatorial chemistry and biology.

Malignant spinal cord compression: prospective study of delays in referral and treatment

Objectives: To examine the delay in presentation, diagnosis, and treatment of malignant spinal cord compression and to define the effect of this delay on motor and bladder function at the time of treatment.

Mechanical behavior in living cells consistent with the tensegrity model

Alternative models of cell mechanics depict the living cell as a simple mechanical continuum, porous filament gel, tensed cortical membrane, or tensegrity network that maintains a stabilizing prestress through incorporation of discrete structural elements that bear compression. Real-time microscopic analysis of cells containing GFP-labeled microtubules and associated mitochondria revealed that living cells behave like discrete structures composed of an interconnected network of actin microfilaments and microtubules when mechanical stresses are applied to cell surface integrin receptors. Quantitation of cell tractional forces and cellular prestress by using traction force microscopy confirmed that microtubules bear compression and are responsible for a significant portion of the cytoskeletal prestress that determines cell shape stability under conditions in which myosin light chain phosphorylation and intracellular calcium remained unchanged. Quantitative measurements of both static and dynamic mechanical behaviors in cells also were consistent with specific a priori predictions of the tensegrity model. These findings suggest that tensegrity represents a unified model of cell mechanics that may help to explain how mechanical behaviors emerge through collective interactions among different cytoskeletal filaments and extracellular adhesions in living cells.

Antagonistic forces generated by myosin II and cytoplasmic dynein regulate microtubule turnover, movement, and organization in interphase cells

Photoactivation of caged fluorescent tubulin was used mark the microtubule (MT) lattice and monitor MT behavior in interphase cells. A broadening of the photoactivated region occurred as MTs moved bidirectionally. MT movement was not inhibited when MT assembly was suppressed with nocodazole or Taxol; MT movement was suppressed by inhibition of myosin light chain kinase with ML7 or by a peptide inhibitor. Conversely, MT movement was increased after inhibition of cytoplasmic dynein with the antibody 70.1. In addition, the half-time for MT turnover was decreased in cells treated with ML7. These results demonstrate that myosin II and cytoplasmic dynein contribute to a balance of forces that regulates MT organization, movement, and turnover in interphase cells.

Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulation at high pressure.

Constant pressure and temperature molecular dynamics techniques have been employed to investigate the changes in structure and volumes of two globular proteins, superoxide dismutase and lysozyme, under pressure. Compression (the relative changes in the proteins' volumes), computed with the Voronoi technique, is closely related with the so-called protein intrinsic compressibility, estimated by sound velocity measurements. In particular, compression computed with Voronoi volumes predicts, in agreement with experimental estimates, a negative bound water contribution to the apparent protein compression. While the use of van der Waals and molecular volumes underestimates the intrinsic compressibilities of proteins, Voronoi volumes produce results closer to experimental estimates. Remarkably, for two globular proteins of very different secondary structures, we compute identical (within statistical error) protein intrinsic compressions, as predicted by recent experimental studies. Changes in the protein interatomic distances under compression are also investigated. It is found that, on average, short distances compress less than longer ones. This nonuniform contraction underlines the peculiar nature of the structural changes due to pressure in contrast with temperature effects, which instead produce spatially uniform changes in proteins. The structural effects observed in the simulations at high pressure can explain protein compressibility measurements carried out by fluorimetric and hole burning techniques. Finally, the calculation of the proteins static structure factor shows significant shifts in the peaks at short wavenumber as pressure changes. These effects might provide an alternative way to obtain information concerning compressibilities of selected protein regions.

The differential adhesion forces of anterior cruciate and medial collateral ligament fibroblasts: effects of tropomodulin, talin, vinculin, and alpha-actinin.

We have determined the effects of tropomodulin (Tmod), talin, vinculin, and alpha-actinin on ligament fibroblast adhesion. The anterior cruciate ligament (ACL), which lacks a functional healing response, and the medial collateral ligament (MCL), a functionally healing ligament, were selected for this study. The micropipette aspiration technique was used to determine the forces needed to separate ACL and MCL cells from a fibronectin-coated surface. Delivery of exogenous tropomodulin, an actin-filament capping protein, into MCL fibroblasts significantly increased adhesion, whereas its monoclonal antibody (mAb) significantly decreased cell adhesiveness. However, for ACL fibroblasts, Tmod significantly reduced adhesion, whereas its mAb had no effect. mAbs to talin, vinculin, and alpha-actinin significantly decreased the adhesion of both ACL and MCL cells with increasing concentrations of antibody, and also reduced stress fiber formation and cell spreading rate as revealed by immunofluorescence microscopy. Disruption of actin filament and microtubule assembly with cytochalasin D and colchicine, respectively, also significantly reduced adhesion in ACL and MCL cells. In conclusion, both ACL and MCL fibroblast adhesion depends on cytoskeletal assembly; however, this dependence differs between ACL and MCL fibroblasts in many ways, especially in the role of Tmod. These results add yet another possible factor in explaining the clinical differences in healing between the ACL and the MCL.

Estudo do processo de formação do cavaco durante o torneamento e sua relação com a microestrutura utilizando o método dos elementos finitos.

O objetivo desse trabalho foi avaliar o processo de formação do cavaco durante o torneamento utilizando simulação numérica pelo método dos elementos finitos. Para realizar o estudo foram definidos dois tipos de aços inoxidáveis austeníticos, um com matriz metálica sem a presença significativa de inclusões, do tipo ABNT 304, e outro com a presença de inclusões não metálicas, do tipo ABNT 303. O estudo foi focado nos mecanismos de formação e ruptura do cavaco, na determinação das forças de usinagem, no campo de tensões, deformações, e temperaturas durante o processo, que foram relacionados com aspectos e características da microestrutura do material. Os resultados obtidos foram comparados com as forças de usinagem experimentais, com a espessura e morfologia do cavaco. O desenvolvimento do trabalho, de acordo com a metodologia adotada, foi realizado em diferentes etapas. Inicialmente foi elaborado e aplicado um modelo de simulação da usinagem considerando o material homogêneo. Em outra etapa, foi realizada a modelagem de uma microestrutura submetida a um estado de tensão e deformação semelhante ao encontrado na simulação da usinagem realizada com material homogêneo. Os resultados mostraram que as partículas das inclusões maiores, alongadas, e em maior quantidade aumentam a tensão e a deformação na microestrutura. As elevadas temperaturas obtidas na usinagem dos aços inoxidáveis austeníticos aumentam a ductilidade dos sulfetos, esses se deformam em compressão junto com a matriz, e têm um efeito limitado como agente de redução dos esforços de usinagem. Por outro lado, os sulfetos facilitam a etapa de ruptura do cavaco em tensões trativas, e tendem a se romper facilitando o processo de quebra.

Geometric 3D point cloud compression

The use of 3D data in mobile robotics applications provides valuable information about the robot’s environment but usually the huge amount of 3D information is unmanageable by the robot storage and computing capabilities. A data compression is necessary to store and manage this information but preserving as much information as possible. In this paper, we propose a 3D lossy compression system based on plane extraction which represent the points of each scene plane as a Delaunay triangulation and a set of points/area information. The compression system can be customized to achieve different data compression or accuracy ratios. It also supports a color segmentation stage to preserve original scene color information and provides a realistic scene reconstruction. The design of the method provides a fast scene reconstruction useful for further visualization or processing tasks.

Adjustable compression method for still JPEG images

There are a large number of image processing applications that work with different performance requirements and available resources. Recent advances in image compression focus on reducing image size and processing time, but offer no real-time solutions for providing time/quality flexibility of the resulting image, such as using them to transmit the image contents of web pages. In this paper we propose a method for encoding still images based on the JPEG standard that allows the compression/decompression time cost and image quality to be adjusted to the needs of each application and to the bandwidth conditions of the network. The real-time control is based on a collection of adjustable parameters relating both to aspects of implementation and to the hardware with which the algorithm is processed. The proposed encoding system is evaluated in terms of compression ratio, processing delay and quality of the compressed image when compared with the standard method.

3DCOMET: 3D compression methods test dataset

The use of 3D data in mobile robotics applications provides valuable information about the robot’s environment. However usually the huge amount of 3D information is difficult to manage due to the fact that the robot storage system and computing capabilities are insufficient. Therefore, a data compression method is necessary to store and process this information while preserving as much information as possible. A few methods have been proposed to compress 3D information. Nevertheless, there does not exist a consistent public benchmark for comparing the results (compression level, distance reconstructed error, etc.) obtained with different methods. In this paper, we propose a dataset composed of a set of 3D point clouds with different structure and texture variability to evaluate the results obtained from 3D data compression methods. We also provide useful tools for comparing compression methods, using as a baseline the results obtained by existing relevant compression methods.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.