Replacements of Pro86 in phage T4 lysozyme extend an alpha-helix but do not alter protein stability.

To investigate the relation between protein stability and the predicted stabilities of individual secondary structural elements, residue Pro86 in an alpha-helix in phage T4 lysozyme was replaced by ten different amino acids. The x-ray crystal structures of seven of the mutant lysozymes were determined at high resolution. In each case, replacement of the proline resulted in the formation of an extended alpha-helix. This involves a large conformational change in residues 81 to 83 and smaller shifts that extend 20 angstroms across the protein surface. Unexpectedly, all ten amino acid substitutions marginally reduce protein thermostability. This insensitivity of stability to the amino acid at position 86 is not simply explained by statistical and thermodynamic criteria for helical propensity. The observed conformational changes illustrate a general mechanism by which proteins can tolerate mutations.

Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme.

The structures of various mutants of T4 lysozyme have been determined in 25 non-isomorphous crystal forms. This provides an unusually diverse data base to compare the structures and dynamics of a closely related set of proteins in different crystal packing environments. In general, the more tightly packed crystals diffract better than those that are highly hydrated although the wild-type crystal form is an exception. The ability of the protein to form a relatively open but stable lattice may help explain why many of the mutants crystallize in this form. In different crystalline environments, the lysozyme molecules associate with 2-fold, 3-fold, 4-fold, and 5-fold symmetry, as well as with various types of screw associations. A "back-to-back" dimeric association, and a "head-to-tail" 2(1) screw association, are especially common, each occurring in more than half a dozen crystal forms. The 4-fold and 5-fold modes of association are closely related and provide an example of quasi-equivalent association as envisaged by Caspar and Klug. In different crystal environments the lysozyme molecules display a range of over 50 degrees in the hinge-bending angle between the amino and carboxy-terminal domains. Large variations in the hinge-bending angle are observed not only for lysozymes with mutations in the hinge region, but for molecules with mutations far from this site. This suggests that hinge-bending is an intrinsic property of the lysozyme molecule and is not an artifact due to mutation. As the hinge-bending angle increases about 15 degrees beyond that seen in wild-type there is a distinct conformations change in the side-chains of five residues in the hinge-bending region. Changes in the backbone are localized near residues 13, 59 and 80, but do not include significant changes in (phi, psi). Comparison of the different structures indicates that crystal contacts perturb the backbone structure of the protein by 0.2 to 0.5 A. These perturbations are of the same magnitude for helices and beta-sheet strands, suggesting that protein structures can be defined and maintained equally well by hydrogen-bonding (i.e. strand-strand) or by non-hydrogen-bonding (i.e. helix-helix) interactions. The discrepancies between the lysozyme structures in different crystallographic environments are in line with other comparisons of independently determined protein crystal structures. They suggest that protein structures in general are subject to low energy changes in conformation of 0.2 to 0.5 A.(ABSTRACT TRUNCATED AT 400 WORDS)

Cumulative site-directed charge-change replacements in bacteriophage T4 lysozyme suggest that long-range electrostatic interactions contribute little to protein stability.

Bacteriophage T4 lysozyme is a basic molecule with an isoelectric point above 9.0, and an excess of nine positive charges at neutral pH. It might be expected that it would be energetically costly to bring these out-of-balance charges from the extended, unfolded, form of the protein into the compact folded state. To determine the contribution of such long-range electrostatic interactions to the stability of the protein, five positively charged surface residues, Lys16, Arg119, Lys135, Lys147 and Arg154, were individually replaced with glutamic acid. Eight selected double, triple and quadruple mutants were also constructed so as to sequentially reduce the out-of-balance formal charge on the molecule from +9 to +1 units. Each of the five single variant proteins was crystallized and high-resolution X-ray analysis confirmed that each mutant structure was, in general, very similar to the wild-type. In the case of R154E, however, the Arg154 to Glu replacement caused a rearrangement in which Asp127 replaced Glu128 as the capping residue of a nearby alpha-helix. The thermal stabilities of all 13 variant proteins were found to be fairly similar, ranging from 0.5 kcal/mol more stable than wild-type to 1.7 kcal/mol less stable than wild-type. In the case of the five single charge-change variants, for which the structures were determined, the changes in stability can be rationalized in terms of changes in local interactions at the site of the replacement. There is no evidence that the reduction in the out-of-balance charge on the molecule increases the stability of the folded relative to the unfolded form, either at pH 2.8 or at pH 5.3. This indicates that long-range electrostatic interactions between the substituted amino acid residues and other charged groups on the surface of the molecule are weak or non-existent. Furthermore, the relative stabilities of the multiple charge replacement mutant proteins were found to be almost exactly equal to the sums of the relative stabilities of the constituent single mutant proteins. This also clearly indicates that the electrostatic interactions between the replaced charges are negligibly small. The activities of the charge-change mutant lysozymes, as measured by the rate of hydrolysis of cell wall suspensions, are essentially equal to that of the wild-type lysozyme, but on a lysoplate assay the mutant enzymes appear to have higher activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Structural and thermodynamic analysis of the packing of two alpha-helices in bacteriophage T4 lysozyme.

Packing interactions in bacteriophage T4 lysozyme were explored by determining the structural and thermodynamic effects of substitutions for Ala98 and neighboring residues. Ala98 is buried in the core of T4 lysozyme in the interface between two alpha-helices. The Ala98 to Val (A98V) replacement is a temperature-sensitive lesion that lowers the denaturation temperature of the protein by 15 degrees C (pH 3.0, delta delta G = -4.9 kcal/mol) and causes atoms within the two helices to move apart by up to 0.7 A. Additional structural shifts also occur throughout the C-terminal domain. In an attempt to compensate for the A98V replacement, substitutions were made for Val149 and Thr152, which make contact with residue 98. Site-directed mutagenesis was used to construct the multiple mutants A98V/T152S, A98V/V149C/T152S and the control mutants T152S, V149C and A98V/V149I/T152S. These proteins were crystallized, and their high-resolution X-ray crystal structures were determined. None of the second-site substitutions completely alleviates the destabilization or the structural changes caused by A98V. The changes in stability caused by the different mutations are not additive, reflecting both direct interactions between the sites and structural differences among the mutants. As an example, when Thr152 in wild-type lysozyme is replaced with serine, the protein is destabilized by 2.6 kcal/mol. Except for a small movement of Val94 toward the cavity created by removal of the methyl group, the structure of the T152S mutant is very similar to wild-type T4 lysozyme. In contrast, the same Thr152 to Ser replacement in the A98V background causes almost no change in stability. Although the structure of A98V/T152S remains similar to A98V, the combination of T152S with A98V allows relaxation of some of the strain introduced by the Ala98 to Val replacement. These studies show that removal of methyl groups by mutation can be stabilizing (Val98----Ala), neutral (Thr152----Ser in A98V) or destabilizing (Val149----Cys, Thr152----Ser). Such diverse thermodynamic effects are not accounted for by changes in buried surface area or free energies of transfer of wild-type and mutant side-chains. In general, the changes in protein stability caused by a mutation depend not only on changes in the free energy of transfer associated with the substitution, but also on the structural context within which the mutation occurs and on the ability of the surrounding structure to relax in response to the substitution.(ABSTRACT TRUNCATED AT 400 WORDS)

Effect of expiratory loading on expiratory duration and pulmonary stretch receptor discharge.

Slowly adapting pulmonary stretch receptors have been hypothesized to be the afferents mediating the vagally dependent, volume-related prolongation of expiratory time (TE) during expiratory loading. It has been further suggested that the vagal component of this prolongation of TE is due to the temporal summation of pulmonary stretch receptor (PSR) activity during expiratory loading. This hypothesis was tested in rabbits exposed to resistive and elastic single-breath expiratory loading while PSR's were simultaneously recorded. Both types of loads resulted in a decreased expired volume (VE) and increased expiratory duration (TE). The TE for resistive loads were significantly greater than for elastic loads for equivalent VE. Thus two different VE-TE relationships were found for resistive and elastic loads. When TE was plotted against the area under the expired volume trajectory, a single linear relationship was observed. PSR activity recorded during expiratory loading increased as VE decreased and TE increased. A single linear relationship resulted when the number of PSR spikes during the expiration was plotted against the associated TE for all types of loads. These findings demonstrate that the volume-related prolongation of TE with single-breath expiratory loads is associated with an increase in PSR discharge. These results support the hypothesis that the vagal component of load-dependent prolongation of TE is a function of both the temporal and spatial summation of PSR activity during the expiratory phase.

Laryngeal and pump muscle activities during CO2 breathing in neonates.

Term human newborns were challenged with a 2-3% CO2 gas mixture during quiet sleep. A common ventilatory response, consisting of increased tidal volume with no change in respiratory frequency or timing, was observed in all eight subjects. Minute ventilation and mean inspiratory and expiratory flow rates were elevated in all eight subjects [38 +/- 8 (SE), 38 +/- 22, and 39 +/- 9%, respectively]. Diaphragm, intercostal, and posterior cricoarytenoid (PCA) muscle activities during inspiration were increased in four of eight, six of eight, and seven of eight subjects, respectively Changes in intercostal and PCA muscle activities correlated with changes in inspiratory flow rates (r = 0.77 and 0.66, respectively). Diaphragmatic braking of expiratory airflow varied between subjects during room air breathing and did not change in six subjects with CO2 breathing. The remaining two subjects increased postinspiratory inspiratory diaphragmatic activity. Baseline expiratory PCA activity was augmented with CO2 breathing in six of eight subjects and correlated with increases in mean expiratory airflow (r = 0.76). The newborn infant is capable of using a variety of breathing strategies to augment tidal volume and minute ventilation, and control of the upper airway appears to be critical in modulating airflow during CO2 breathing.

Responses of pulmonary vagal mechanoreceptors to high-frequency oscillatory ventilation.

The discharge of 57 slowly adapting pulmonary stretch receptors (PSR's) and 16 rapidly adapting receptors (RAR's) was recorded from thin vagal filaments in anesthetized dogs. The receptors were localized and separated into three groups: extrathoracic tracheal, intrathoracic tracheal, and intrapulmonary receptors. The influence of high-frequency oscillatory ventilation (HFO) at 29 Hz on receptor discharge was analyzed by separating the response to the associated shift in functional residual capacity (FRC) from the oscillatory component of the response. PSR activity during HFO was increased from spontaneous breathing (49%) and from the static FRC shift (25%). PSR activity during the static inflation was increased 19% over spontaneous breathing. RAR activity was also increased with HFO. These results demonstrate that 1) the increased activity of PSR and RAR during HFO is due primarily to the oscillating action of the ventilator and secondarily to the shift in FRC associated with HFO, 2) the increased PSR activity during HFO may account for the observed apneic response, and 3) PSR response generally decreases with increasing distance from the tracheal opening.

Posterior cricoarytenoid and diaphragm activities during tidal breathing in neonates.

To investigate airflow regulation in newborn infants, we recorded airflow, volume, diaphragm (Di), and laryngeal electromyogram (EMG) during spontaneous breathing in eight supine unsedated sleeping full-term neonates. Using an esophageal catheter electrode, we recorded phasic respiratory activity consistent with that of the principal laryngeal abductors, the posterior cricoarytenoids (PCA). Sequential activation of PCA and Di preceded inspiration. PCA activity typically peaked early in inspiration followed by either a decrescendo or tonic EMG activity of variable amplitude during expiration. Expiratory airflow retardation, or braking, accompanied by expiratory prolongation and reduced ventilation, was commonly observed. In some subjects we observed a time interval between PCA onset and a sudden increase in expiratory airflow just before inspiration, suggesting that release of the brake involved an abrupt loss of antagonistic adductor activity. Our findings suggest that airflow in newborn infants is controlled throughout the breathing cycle by the coordinated action of the Di and the reciprocal action of PCA and laryngeal adductor activities. We conclude that braking mechanisms in infants interact with vagal reflex mechanisms that modulate respiratory cycle timing to influence both the dynamic maintenance of end-expiratory lung volume and ventilation.

Reflex control of inspiratory duration in newborn infants.

We applied graded resistive and elastic loads and total airway occlusions to single inspirations in six full-term healthy infants on days 2-3 of life to investigate the effect on neural and mechanical inspiratory duration (TI). The infants breathed through a face mask and pneumotachograph, and flow, volume, airway pressure, and diaphragm electromyogram (EMG) were recorded. Loads were applied to the inspiratory outlet of a two-way respiratory valve using a manifold system. Application of all loads resulted in inspired volumes decreased from control (P less than 0.001), and changes were progressive with increasing loads. TI measured from the pattern of the diaphragm EMG (TIEMG) was prolonged from control by application of all elastic and resistive loads and by total airway occlusions, resulting in a single curvilinear relationship between inspired volume and TIEMG that was independent of inspired volume trajectory. In contrast, when TI was measured from the pattern of airflow, the effect of loading on the mechanical time constant of the respiratory system resulted in different inspired volume-TI relationships for elastic and resistive loads. Mechanical and neural inspired volume and duration of the following unloaded inspiration were unchanged from control values. These findings indicate that neural inspiratory timing in infants depends on magnitude of phasic volume change during inspiration. They are consistent with the hypothesis that termination of inspiration is accomplished by an "off-switch" mechanism and that inspired volume determines the level of vagally mediated inspiratory inhibition to trigger this mechanism.

Reflex control of expiratory duration in newborn infants.

We investigated the effect on expiratory duration (TE) of application of graded resistive and elastic loads and total airway occlusions to single expirations in 9 full-term healthy infants studied on the 2nd or 3rd day of life. The infants breathed through a face mask and pneumotachograph, and flow, volume, airway pressure, and diaphragm electromyogram (EMG) were recorded. Loads were applied to the expiratory outlet of a two-way respiratory valve using a manifold system. Application of all loads resulted in expired volumes (VE) decreased from control (P less than 0.05), and changes were progressive with increasing loads. As VE became smaller, end-expiratory volume (EEV) became greater. TE, measured either from the pattern of airflow or airway pressure, or from diaphragm EMG activity, progressively increased with increasing loads and was greatest with total occlusions (P less than 0.05, compared with control). Resistive loading resulted in a greater accumulated VE history than elastic loading to the same EEV. For equivalent changes in EEV, TE was more prolonged with resistive than with elastic loading. Expiratory loading did not change the inspiratory duration determined from the diaphragm EMG activity of the breath immediately following each loaded expiration. These findings in infants are consistent with an integrative neural mechanism that modulates TE in response to the accumulated VE history, including both EEV and rate of lung deflation.

Laryngeal and diaphragmatic muscle activities and airflow patterns after birth in premature lambs.

The nature and control of early neonatal respiratory patterns were determined in 10 premature, asphyxiated lambs. Severe retardation of early expiratory airflow (braking) characterized an initial pattern (A), but was absent in a final one (B). During a transition pattern (pattern T), pattern A and B airflow types occurred. Close temporal relationships between the airflow patterns and posterior cricoarytenoid (PCA), thyroarytenoid (TA), and diaphragm (D) integrated muscle activities were demonstrated quantitatively. Specifically, in pattern A, the duration of braked expiratory airflow was related to the durations of TA burst activity and the absence of PCA burst activity (r2 = 0.99). In pattern A, pH, but not arterial PCO2 or arterial PO2, differed from that in patterns T and B [7.01 +/- 0.14 (A), 7.11 +/- 0.12 (T), 7.19 +/- 0.08 (B) (P < 0.03)]. Within-breath airflow and respiratory muscle activity relationships and differences in neural and mechanical respiratory timing intervals between patterns suggested that neural feedback was important in the control of central pattern generation. Thus activities of PCA, TA, and D shape the early neonatal airflow patterns and are influenced mainly by neuromechanical, and not chemical, feedback.

Multiresolution segmentation of respiratory electromyographic signals.

Analysis of respiratory electromyographic (EMG) signals in the study of respiratory control requires the detection of burst activity from background (signal segmentation), and focuses upon the determination of onset and cessation points of the burst activity (boundary estimation). This paper describes a new automated multiresolution technique for signal segmentation and boundary estimation. During signal segmentation, a new transitional segment is defined which contains the boundary between background and burst activity. Boundary estimation is then performed within this transitional segment. Boundary candidates are selected and a probability is attributed to each candidate, using an artificial neural network. The final boundary for a given transitional segment is the boundary estimate with the maximum a posteriori probability. This new method has proved accurate when compared to boundaries chosen by two investigators.

Ventilatory and timing parameters in normal horses at rest up to age one year.

The purpose of the study was to document the developmental changes in the ventilatory and timing parameters associated with quiet breathing at rest in awake, standing horses during the first year post partum. Tidal volume (VT), breathing frequency, airflow, mechanical timing intervals and minute ventilation (VE) were measured serially in foals age 24 h-1 year. In the growing foal, VE increased due to a progressive rise in VT, in spite of a pronounced decrease in respiratory frequency. When normalised to body weight (bwt), VE/kg declined with maturation in a curvilinear fashion, from mean +/- s.d. 848 +/- 231 ml/min/kg in the 24 h-old foal, to 155 +/- 15 ml/kg/min in the 1-year-old foal. Tidal volume normalised to bwt remained relatively constant during the study period, with the exception that at age 3 weeks and from 2-6 months, VT/kg was significantly lower than the value recorded at age 1 week. The decrease in frequency resulted from prolongation of both inspiratory (TI) and expiratory (TE) time but there was a disproportionately larger increase in TE compared to TI, which resulted in a significantly lower ratio of TI/TE in older foals. The allometric equation relating VT to bwt suggested that lung growth in the horse is dysanaptic, with increases in overall body size exceeding lung growth in the maturing foal during the first year post partum.

Changes in breathing pattern in the normal horse at rest up to age one year.

Changes in pattern of airflow, sequence of respiratory muscle activation and generated pressures were measured serially in a group of foals during the first year post partum, in order to describe the maturation of the equine breathing pattern. In neonatal foals, inspiration and expiration were both primarily active and airflow pattern was essentially monophasic. By age 1 year, foals displayed essentially the same breathing pattern previously described in adult horses, utilising a combination of active and passive inspiration and expiration to breathe around, rather than from, the relaxation volume of the respiratory system (Vrx). A strong temporal relationship during growth was found between the timing of changes observed in airflow pattern and in the neuromuscular strategy of breathing. The transition to the adult breathing pattern appeared to involve a time delay in activation of both inspiratory and expiratory muscle groups, establishing a passive and active component to both inspiration and expiration. Throughout the study period, concurrent with the increase in delay of abdominal muscle activation, the expiratory flow pattern became progressively more biphasic in appearance. The time of appearance of a consistent biphasic inspiratory flow pattern was considerably later, at approximately age 1 year and coincided with the appearance of a delay in inspiratory muscle activation. From our results, we conclude that the transition from the neonatal to the adult breathing strategy in the horse appears not to be induced by the time course of chest wall stiffening during maturation. While changes in relative body proportions and size of abdominal contents during growth may influence the transition in breathing, our results also indicate that respiratory control mechanisms play an essential role in the expression of the polyphasic breathing pattern.

Endotracheal measurement of thyroarytenoid activity in newborn lambs.

Laryngeal control of expiratory airflow is a principal means by which the newborn establishes and maintains absolute lung volume. Specifically, retardation of expiratory airflow is effected by the major adductors of the larynx, the thyroarytenoid (TA) muscles. The long-term aim of this research is to determine if monitoring TA activity can be used to optimize absolute lung volume during artificial ventilation of the human baby. This initial study, performed in unanesthetized chronically instrumented newborn lambs, tests the hypothesis that the timings of the onsets, peaks and durations of TA activity recorded by the endotracheal electrode are equivalent to those measured by a surgically placed intramuscular electrode. Endotracheal measurement of TA activity is accurate and specific and can monitor changes in airway pressure and lung volume.

A genetic screen for mutations that increase the thermal stability of phage T4 lysozyme.

A method has been developed to screen for mutants of phage T4 lysozyme that are more stable than the wild-type enzyme. Using an assay that detects lysozyme activity on Petri plates [Streisinger, G., Okada, Y., Emrich, J., Newton, J., Tsugita, A., Terzaghi, E. & Inouye, M. (1966) Cold Spring Harbor Symp. Quant. Biol. 31, 77-84], protein synthesized during the formation of phage plaques at a permissive temperature (33 degrees C) was tested for its ability to withstand incubation at a temperature that inactivates the wild-type enzyme. In our initial screen of approximately 3 X 10(4) plaques from a T4 phage stock mutagenized with hydroxylamine, greater than 30 mutants that produce lysozyme activity resistant to high temperature incubation were found. Lysozyme produced by two of the mutants was purified and found to denature at a higher temperature than the wild-type enzyme in vitro. We have called such mutants "st" for thermostable. The existence of st mutants indicates that protein stability is not maximized during evolution; instead, it is likely that stability is optimized for the physiology of the organism. Analysis of the structures of these mutants will provide another way to identify and predict interactions that stabilize proteins. The method of finding thermostable variants presented here may be applicable to any protein that can be detected by a plate assay or by a plate screen with antibodies.

Respiratory mechanics of the horse during the first year of life.

This study investigated the developmental changes in the mechanical properties of the respiratory system in growing horses. Pulmonary mechanics and lung volumes were serially measured in anesthetized foals during the first year of life. Quasi-static pressure-volume curves were generated, and functional residual capacity (FRC) was measured using a closed nitrogen equilibration technique. At birth, chest wall compliance normalized to body weight was substantially less than that reported in other less precocious newborn species, while lung compliance normalized to body weight was similar to values reported for other species. Characteristics of the transition from the neonatal to adult respiratory system in the foal included a decrease in the ratios of chest wall to lung compliance (Cw/CL) and the unstressed volume of the chest wall to TLC, and a constant FRC/TLC throughout most of the study period. The somatic growth of the foal and its respiratory system were uneven processes, with increases in lung volume lagging increases in overall body size.

Perturbation of Trp 138 in T4 lysozyme by mutations at Gln 105 used to correlate changes in structure, stability, solvation, and spectroscopic properties.

In order to correlate between spectroscopic and structural changes in a protein, the environment of Trp 135 in T4 lysozyme was deliberately perturbed by the replacement of Gln 105 with alanine (Q105A), glycine (Q105G), and glutamic acid (Q105E). In wild-type lysozyme, Trp 135 is buried, but the indole nitrogen is hydrogen-bonded to the side-chain of Gln 105. In the Q105G and Q105A mutant structures, the indole nitrogen becomes accessible to solvent. Crystallographic analysis shows that the structures of all of the mutants are similar to wild-type. There are, however, distinct rearrangements of the local solvent structure in response to the new side-chains. There are also small but significant changes in the relative orientations of the two domains of the protein that appear to result from a series of small, concerted movements of side-chains adjacent to residue 105. Evaluation of the fluorescence and phosphorescence of the mutant proteins in terms of their observed three-dimensional structures shows that large spectral changes do not necessarily imply large changes in structure or in static solvent accessibility. Increases in polar relaxation about the excited state of tryptophan may be the result of only small increases in local dynamics or solvent exposure. 1H-NMR was also used to monitor the effects of the substitutions on Trp 138. In Q105E, but not in Q105G, Q105A and WT, the H epsilon chemical shift of Trp 138 is very pH-dependent, apparently reflecting the titration of Glu 105 which has a spectroscopically determined pKa of 6.0. The elevation of the pKa of Glu 105 in Q105E is also reflected in the pH dependence of the stability of this mutant.

Correlation between mutational destabilization of phage T4 lysozyme and increased unfolding rates.

The thermodynamics and kinetics of unfolding of 28 bacteriophage T4 lysozyme variants were compared by using urea gradient gel electrophoresis. The mutations studied cause a variety of sequence changes at different residues throughout the polypeptide chain and result in a wide range of thermodynamic stabilities. A striking relationship was observed between the thermodynamic and kinetic effects of the amino acid replacements: All the substitutions that destabilized the native protein by 2 kcal/mol or more also increased the rate of unfolding. The observed increases in unfolding rate corresponded to a decrease in the activation energy of unfolding (delta Gu) at least 35% as large as the decrease in thermodynamic stability (delta Gu). Thus, the destabilizing lesions bring the free energy of the native state closer to that of both the unfolded state and the transition state for folding and unfolding. Since a large fraction of the mutational destabilization is expressed between the transition state and the native conformation, the changes in folding energetics cannot be accounted for by effects on the unfolded state alone. The results also suggest that interactions throughout much of the folded structure are altered in the formation of the transition state during unfolding.

A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene.

The hydrophobic cores of proteins are generally well packed, with few cavities. Mutations in which a bulky buried residue such as leucine or phenylalanine is replaced with a small residue such as alanine can create cavities in the core of a protein (our unpublished results). The sizes and shapes of such cavities can vary substantially depending on factors such as local geometry, whether or not a cavity already exists at the site of substitution, and the degree to which the protein structure relaxes to occupy the space vacated by the substituted residue. We show by crystallographic and thermodynamic analysis that the cavity created by the replacement Leu 99----Ala in T4 lysozyme is large enough to bind benzene and that ligand binding increases the melting temperature of the protein by 6.0 degrees C at pH 3.0. Benzene does not, however, bind to the cavity created by the Phe 153----Ala replacement. The results show that cavities can be engineered in proteins and suggest that such cavities might be tailored to bind specific ligands. The binding of benzene at an internal site 7 A from the molecular surface also illustrates the dynamic nature of proteins, even in crystals.