I. Introduction to Carbonic Anhydrase (CA) and to the Review 948 1. Introduction: Overview of CA as a Model 948 1.1. Value of Models 950 1.2. Objectives and Scope of the Review 950 2. Overview of Enzymatic Activity 950 3. Medical Relevance 951 II. Structure and Structure−Function Relationships of CA 953 4. Global and Active-Site Structure 953 4.1. Structure of Isoforms 953 4.2. Isolation and Purification 954 4.3. Crystallization 954 4.4. Structures Determined by X-ray Crystallography and NMR 955 4.4.1. Structures Determined by X-ray Crystallography 955 4.4.2. Structure Determined by NMR 955 4.5. Global Structural Features 963 4.6. Structure of the Binding Cavity 964 4.7. Zn II -Bound Water 965 5. Metalloenzyme Variants 966 6. Structure−Function Relationships in the Catalytic Active Site of CA 968 6.1. Effects of Ligands Directly Bound to Zn II 968 6.2. Effects of Indirect Ligands 969 7. Physical-Organic Models of the Active Site of CA 969 III. Using CA as a Model to Study Protein−Ligand Binding 970 8. Assays for Measuring Thermodynamic and Kinetic Parameters for Binding of Substrates and Inhibitors 970 8.1. Overview 970 8.

This manuscript describes the fabrication and use of a three-dimensional magnetic trap for diamagnetic objects in an aqueous solution of paramagnetic ions; this trap uses permanent magnets. It demonstrates trapping of polystyrene spheres, and of various types of living cells: mouse fibroblast ͑NIH-3T3͒, yeast (Saccharomyces cerevisiae), and algae (Chlamydomonas reinhardtii). For a 40 mM solution of gadolinium (III) diethylenetriaminepentaacetic acid ͑Gd· DTPA͒ in aqueous buffer, the smallest cell (particle) that could be trapped had a radius of ϳ2.5 m. The trapped particle and location of the magnetic trap can be translated in three dimensions by independent manipulation of the permanent magnets. This letter a1so characterizes the biocompatibility of the trapping solution.The ability to position cells, on surfaces and in suspension, is broadly useful in cellular biology. Microcontact printing of self-assembled monolayers 1-3 and other techniques of surface engineering 4,5 are used for confining and controlling the mobility of cells on surfaces. Optical traps can confine and manipulate cells and microspheres in suspension, and have been used to determine the elasticity of the cell membrane, 6-8 to observe cell division, 9 to measure inhibition of cell adhesion, 10 and to strain cells to induce activity in signaling pathways. 11 While optical traps have enabled many experiments in biophysics, they also have limitations. The laser power required to trap a micron-sized particle (for example, a cell) is proportional to the ratio of the refractive index of the particle to that of the medium. 12 Since the ratio of the refractive indices for most biological materials to biocompatible fluid media is near unity, trapping requires lasers having powers up to ϳ100 mW. This high laser power can raise the local temperature in the liquid by several degrees, 13 and this heating can damage or kill a trapped cell. In addition, traditional optical tweezers cannot trap objects with ratios of refractive indices of the object to the environment of less than unity (e.g., a gas-filled glass sphere in water 14 or a water drop in liquid parafilm 15 ) or greater than 1.5 (e.g., diamond particles in water). 16 Optical tweezers are restrictive in the size of the particle that can be trapped; particles must be ഛ10 m in diameter. The trapping force of optical tweezers is minimal outside the focus of the laser beam, requiring objects to enter the focus of the laser before they can be trapped. The small capture volume for many particles (only a few cubic microns) results in significant waiting periods before objects are trapped in dilute samples. The short working distance of the objective lens used to focus the light restricts the trap to regions near ͑Ͻ200 m͒ the surface. The high-powered lasers and infinity-corrected, high numerical aperture objectives used to construct an optical trap are expensive.Although the use of magnetism to manipulate objects was described by Thales ͑c.500 B.C.͒, the trapping of objects in a stable magnetic equilibrium...

This paper describes the fabrication of a fluidic device for detecting and separating diamagnetic materials that differ in density. The basis for the separation is the balance of the magnetic and gravitational forces on diamagnetic materials suspended in a paramagnetic medium. The paper demonstrates two applications of separations involving particles suspended in static fluids for detecting the following: (i) the binding of streptavidin to solid-supported biotin and (ii) the binding of citrate-capped gold nanoparticles to amine-modified polystyrene spheres. The paper also demonstrates a microfluidic device in which polystyrene particles that differ in their content of CH2Cl groups are continuously separated and collected in a flowing stream of an aqueous solution of GdCl3. The procedures for separation and detection described in this paper require only gadolinium salts, two NdFeB magnets, and simple microfluidic devices fabricated from poly(dimethylsiloxane). This device requires no power, has no moving parts, and may be suitable for use in resource-poor environments.

This paper shows that proteins display an unexpectedly wide range of behaviors in buffers containing moderate (0.1-10 mM) concentrations of SDS (complete unfolding, formation of stable intermediate states, specific association with SDS, and various kinetic phenomena); capillary electrophoresis provides a convenient method of examining these behaviors. Examination of the dynamics of the response of proteins to SDS offers a way to differentiate and characterize proteins. Based on a survey of 18 different proteins, we demonstrate that proteins differ in the concentrations of SDS at which they denature, in the rates of unfolding in SDS, and in the profiles of the denaturation pathways. We also demonstrate that these differences can be exploited in the analysis of mixtures.capillary electrophoresis ͉ surfactant ͉ intermediates ͉ kinetics T his manuscript surveys the range of electrophoretic behaviors observed for proteins in solutions containing SDS at concentrations below those used in SDS͞PAGE. The aggressive conditions used to prepare proteins for characterization by SDS͞PAGE (1) are designed to produce completely denatured, unfolded aggregates of protein and SDS; less forcing conditions have generally been ignored. Because SDS͞PAGE uses forcing conditions, it has failed to reveal the wealth of information available from systems of protein and SDS: information about the kinetics of denaturation; about previously undetected, stable aggregates of protein and SDS with reasonably well defined stoichiometry; and about intermediates along the pathway to the fully denatured aggregates of protein and SDS.Intermediates in the denaturation of some proteins with SDS have been identified: RNase A (2), cytochrome c that had been denatured in acid (3), BSA (4), and mushroom tyrosinase (5). Many proteins have a ''low'' state, in which the protein binds a few molecules of SDS, and ''high'' state, in which the protein binds one molecule of SDS per two amino acids (6, 7). These studies have concentrated mostly on single proteins or on the similarities between proteins and have not demonstrated or exploited the wide variability in behavior of proteins as they are denatured in SDS.We find that proteins show large differences in the concentrations of SDS and in the rates at which they change conformation and unfold in SDS, in the concentrations of SDS at which intermediates form along the unfolding pathway, and in the number of these intermediates. [We use the term ''rate'' to refer to the kinetics of unfolding of the native protein. With this technique, we can only estimate the time scale for unfolding of a protein at a particular concentration of SDS qualitatively, i.e., estimate whether it is shorter, similar, or longer than the time of the capillary electrophoresis (CE) experiment.] These differences among proteins can be exploited to provide the basis for a method of differentiating (and in some instances separating) proteins and information about the relations between their structure and stabilities. We believe that this procedu...

This study compares the rate of denaturation with sodium dodecyl sulfate (SDS) of the individual rungs of protein charge ladders generated by acylation of the lysine epsilon-NH3+ groups of bovine carbonic anhydrase II (BCA). Each acylation decreases the number of positively charged groups, increases the net negative charge, and increases the hydrophobic surface area of BCA. This study reports the kinetics of denaturation in solutions containing SDS of the protein charge ladders generated with acetic and hexanoic anhydrides; plotting these rates of denaturation as a function of the number of modifications yields a U-shaped curve. The proteins with an intermediate number of modifications are the most stable to denaturation by SDS. There are four competing interactions-two resulting from the change in electrostatics and two resulting from the change in exposed hydrophobic surface area-that determine how a modification affects the stability of a rung of a charge ladder of BCA to denaturation with SDS. A model based on assumptions about how these interactions affect the folded and transition states has been developed and fits the experimental results. Modeling indicates that for each additional acylation, the magnitude of the change in the activation energy of denaturation (DeltaDeltaG(double dagger)) due to changes in the electrostatics is much larger than the change in DeltaDeltaG(double dagger) due to changes in the hydrophobicity, but the intermolecular and intramolecular electrostatic effects are opposite in sign. At the high numbers of acylations, hydrophobic interactions cause the hexanoyl-modified BCA to denature nearly three orders of magnitude more rapidly than the acetyl-modified BCA.