Effects of repeated injection of cyclosporin A on pentylenetetrazol-induced convulsion and cyclophilin mRNA levels in rat brain

To investigate the relationship between the immune system and convulsions in an animal model, we examined the effects of repeated administration with the immunosuppressant cyclosporin A on pentylenetetrazol (PTZ)-induced convulsions and the changes in the mRNA expression of its binding protein cyclophilin in the rat brain. The consecutive administration of cyclosporin A (5 mg/kg, s.c., 14 days) significantly aggravated the severity of convulsions induced with PTZ 75 mg/kg, i.p. Furthermore, it down-regulated the levels of cyclophilin mRNA in several brain regions and inhibited the PTZ-induced increase of hippocampal cyclophilin mRNA. Compared with the group without PTZ pretreatment or the group treated with chronic vehicle administration after the PTZ-preinjection, chronic cyclosporin A administration after the initial injection of PTZ apparently aggravated convulsions after the second PTZ injection. Interestingly, the increase in hippocampal cyclophilin mRNA observed after a single PTZ injection was not found after the second PTZ injection in the group with PTZ pretreatment. Therefore, these findings suggest that cyclosporin A administered peripherally can affect the central nervous system, and that an immune response associated with the first convulsive episode plays a key role in severity during subsequent attacks.     

Interactions of cyclophilin with the mitochondrial inner membrane and regulation of the permeability transition pore, and cyclosporin A-sensitive channel

Mammalian mitochondria possess an inner membrane channel, the permeability transition pore (MTP), which can be inhibited by nanomolar concentrations of cyclosporin (CS) A. The molecular basis for MTP inhibition by CSA remains unclear. Mitochondria also possess a matrix cyclophilin (CyP) with a unique N-terminal sequence (CyP-M). To test the hypothesis that it interacts with the MTP, we have studied the interactions of CyP-M with rat liver mitochondria by Western blotting with a specific antibody against its unique N terminus. Although sonication in isotonic sucrose at pH 7.4 refraction sediments with submitochondrial particles at 150,000 x g. We show that the interactions of this CyP-M pool with submitochondrial particles are disrupted (i) by the addition of CSA, which inhibits the pore, but not of CSH, which does not, and (ii) by acidic pH condition, which also leads to selective inhibition of the MTP; furthermore, we show that the effect of acidic pH on CyP-M fully prevents the inhibitory effect of H+ on the MTP (Nicolli, A., Petronilli, V., and Bernardi, P. (1993) Biochemistry 32, 4461-4465). These data suggest that CyP-M inhibition by CSA and protons may be due to unbinding of CyP-M from its putative binding site on the MTP. A role for CyP-M in MTP regulation is also supported by a study with a series of CSA derivatives with graded affinity for CyP. We show that with each derivative the isomerase activity of CyP-M purified to homogeneity is similar to that displayed at inhibition of MTP opening, CyP-M (but not CyP-A) and decreased efficiency at MTP inhibition is obtained by substitution in position 8 while a 4-substituted, nonimmunosuppressive derivative is a as effective as the native CSA molecule, indicating that calcineurin is not involved in MTP inhibition by CSA.     

Comparative binding studies of cyclophilins to cyclosporin A and derivatives by fluorescence measurements

The interaction of cyclosporin A and cyclosporin derivatives with cyclophilins A, B, and C has been investigated by means of fluorescence measurement techniques. Since Trp-121 of cyclophilin A is in close contact with bound cyclosporins and changes its fluorescence emission upon binding, direct estimation of Kd values for cyclosporins is straightforward in this case. Cyclophilins B and C, however, display no evident binding-dependent fluorescence changes suitable for the estimation of their binding affinities. This problem can be circumvented by measuring the variations of fluorescence emission intensities of a mixture of cyclophilin A and the fluorescence measurements unsuitable for cyclosporin binder as a function of ligand concentration. Application of a mixed-mode kinetic analysis then allows the calculation of the cyclosporin binding affinity of the second binder in the system. The dissociation constant for cyclosporin A/cyclophilin A was found to be 36.8 nM. Mixed-mode kinetic calculations yielded Kd values of 9.8 and 90.8 nM for cyclophilins B and C, respectively. The analysis was extended to noncyclophilin (weak) cyclosporin binders such as calmodulin and actin, resulting in approximate Kd values of 1.2 and 5.7 microM, respectively. Using the same approach, the Kd values of a series of different cyclosporin derivatives were determined.     

Similarities and differences between human cyclophilin A and other beta-barrel structures. Structural refinement at 1.63 A resolution

The structure of the unligated recombinant human cyclophilin A (CyP A) has been refined to an R-factor of 0.18 at 1.63 A resolution. The root-mean-squared deviations of the refined structure are 0.013 A and 2.50 degrees from ideal geometries of bond length and bond angle, respectively. Eight antiparallel beta-strands of CyP A form a right-handed beta-barrel. The structure of CyP A is compared with other members in the antiparallel eight-stranded beta-barrel family and with the parallel eight-stranded alpha/beta barrels. Although all known eight-stranded barrels are right-handed, the tilted angle of the strands against the barrel axis varies from 45 degrees for retinol binding protein and 49 degrees for CyP A to 70 degrees for superoxide dismutase. As a result, the beta-barrel of CyP A is not completely superimposable with other members of beta-barrels. The structure of CyP A has a unique topology, distinct from other members in the beta-barrel family. In addition, CyP A is a closed beta-barrel so that neither the immunosuppressive drug cyclosporin A (CsA) nor the proline-containing substrate can bind to the hydrophobic core of the CyP A barrel, while the hydrophobic core of most other barrels is open for ligation. These observations probably indicate that CyP A is neither functionally nor evolutionally related to other beta-barrel structures. Details of interactions between solvent molecules and the active site residues of CyP A are illustrated. A water-co-operated mechanism, where the cis<-->trans isomerization might possibly consist of (1) transition of the prolyl bond and (2) release of N or C-terminal residues of substrate from CyP, is addressed. The refined structure reveals no disulfide bridges in CyP A. Cys115 is near the CsA site, but unlikely to be directly involved in CsA binding because of steric hindrance from Thr119 and Leu122. This geometry probably rules out any mechanisms involving a tetrahedral intermediate formed between cysteine and substrate during cis<-->trans isomerization.     

Characterization of the cyclophilin gene family of Arabidopsis thaliana and phylogenetic analysis of known cyclophilin proteins

We have isolated four members of the Arabidopsis cyclophilin (CyP) gene family, designated ROC1 to ROC4 (rotamase CyP). Deduced peptides of ROC1, 2 and 3 are 75% to 91% identical to Brassica napus cytosolic CyP, contain no leader peptides and include a conserved seven amino-acid insertion relative to mammalian cytosolic CyPs. Two other Arabidopsis CyPs, ROC5 (43H1; ATCYP1) and ROC6 (ATCYP2), share these features. ROC1, ROC2, ROC3 and ROC5 are expressed in all tested organs of light-grown plants. ROC2 and ROC5 show elevated expression in flowers. Expression of ROC1, ROC2, and ROC3 decreases in darkness and these genes also exhibit small elevations in expression upon wouding. The five Arabidopsis genes encoding putative cytosolic CyPs (ROC1, 2, 3, 5 and 6) contain no introns. In contrast, ROC4, which encodes a chloroplast stromal CyP, is interrupted by six introns. ROC4 is not expressed in roots, and is strongly induced by light. Phylogenetic trees of all known CyPs and CyP-related proteins provide evidence of possible horizontal transfer of CyP genes between prokaryotes and eukaryotes and of a possible polyphyletic origin of these proteins within eukaryotes. These trees also show significant grouping of eukaryotic CyPs on the basis of subcellular localization and structure. Mitochondrial CyPs are closely related to cytosolic CyPs of the source organism, but endoplasmic reticulum CyPs form separate clades. Known plant CyPs fall into three clades, one including the majority of higher-plant cytosolic CyPs, one including only ROC2 and a related rice CyP, and one including only chlorplast CyPs.     

Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment

The structure and expression pattern of a human gene located within a homozygously deleted region of a metastatic prostate cancer have been characterized. Multiple cDNA fragments of this gene were isolated by hybrid capture with yeast artificial chromosome clones covering the deletion region. Eleven coding exons spanned 205-220 kb of the 730- to 970-kb deletion. The predicted amino acid sequence was 43% identical to that of an anonymous Caenorhabditis elegans gene and 20% identical to an accessory or regulatory subunit of the oligosaccharyltransferase enzyme complex in Saccharomyces cerevisiae. Hydrophobicity profiles of all three gene products were similar and showed four putative membrane-spanning domains in the molecules' C-terminal halves, suggesting a general conservation of function. The gene was expressed as an approximately 1.5-kb mRNA in most nonlymphoid human cells/tissues including prostate, lung, liver, and colon. Expression was detected in many epithelial tumor cell lines, but was undetectable by Northern blot or RT-PCR in 14 of 15 colorectal, 1 of 8 lung, and 1 of 4 liver cancer cell lines. Lack of expression in tumor cell lines was highly correlated with hypermethylation of a CpG island located at the gene's 5' end. These findings form a basis for further work on this candidate tumor suppressor gene.     

X-ray crystal structure of the yeast Kar3 motor domain complexed with Mg.ADP to 2.3 A resolution

The kinesin family of motor proteins, which contain a conserved motor domain of approximately 350 amino acids, generate movement against microtubules. Over 90 members of this family have been identified, including motors that move toward the minus or plus end of microtubules. The Kar3 protein from Saccharomyces cerevisiae is a minus end-directed kinesin family member that is involved in both nuclear fusion, or karyogamy, and mitosis. The Kar3 protein is 729 residues in length with the motor domain located in the C-terminal 347 residues. Recently, the three-dimensional structures of two kinesin family members have been reported. These structures include the motor domains of the plus end-directed kinesin heavy chain [Kull, F. J., et al. (1996) Nature 380, 550-555] and the minus end-directed Ncd [Sablin, E. P., et al. (1996) Nature 380, 555-559]. We now report the structure of the Kar3 protein complexed with Mg.ADP obtained from crystallographic data to 2.3 A. The structure is similar to those of the earlier kinesin family members, but shows differences as well, most notably in the length of helix alpha 4, a helix which is believed to be involved in conformational changes during the hydrolysis cycle.     

The X-ray structure of a divergent cyclophilin from the nematode parasite Brugia malayi

The following is a review of an emerging topic in the literature which has led to new hypotheses regarding the mechanisms of pathogenesis of the various tissue specific AIDS associated syndromes. The fundamental hypothesis in this review proposes that HIV-1 is able to increase lymphocyte and monocyte localization in tissues where released HIV-1 proteins cause local tissue damage leading to any one of the various AIDS associated syndromes. It is also hypothesized here that syndromes associated with other lymphotrophic viruses result from the ability of these viruses to direct leukocyte extravasation of blood vessel walls and to initiate tissue specific pathogenesis. Further, it is suggested here that new concepts and strategies for delivering gene therapy to specific tissues can be derived from our understanding of the mechanisms through which lymphotrophic viruses localize in specific tissues. HIV-1 infection of lymphocytes and monocytes leads to increased adhesion of these cells to vascular endothelium and extracellular matrix molecules. In addition, HIV-1 infection of various leukocytes leads to increased secretion of extracellular matrix degrading matrix metalloproteinases. Increases in leukocyte adhesion and matrix metalloproteinase secretion are associated with the normal mechanisms through which leukocytes localize in tissues during inflammation. The ability of HIV-1 to activate leukocyte adhesion and matrix metalloproteinase secretion suggests that HIV-1 has evolved a way to take advantage of leukocyte inflammatory mechanisms in order to exit the blood stream and gain access to body tissues. The ability of HIV-1 to use infected cells to localize in various tissues may lead to the establishment of HIV-1 reservoirs in tissues. Such viral reservoirs may cause the various tissue specific AIDS associated syndromes. AIDS patients have been found to have elevated adhesion molecules (integrins, and cell adhesion molecules or CAMs) on their peripheral blood lymphocytes (PBLs). While there is little clinical evidence that the tissue localization of HIV-1 infected leukocytes are the cause of the HIV-1 related syndromes, studies in vitro and with animal models have shown that the HIV-1 gene products Tat, Rev and gp120 are potent neurotoxins. It has also been shown that Tat can contribute to the growth of cells from Kaposi's sarcoma lesions. Further, HIV-1 infected cells have been shown to secrete cytotoxic levels of a variety of growth factors and small molecules. Thus, it is likely that the localization of HIV-1 infected cells in specific tissues could contribute to the HIV-1 associated syndromes such as AIDS dementia, HIV-1 related interstitial lung disease, HIV-1 associated nephropathy, the HIV-1 wasting syndrome and perhaps AIDS associated Kaposi's sarcoma and hyperproliferative skin disorders. This review will examine studies in the literature which demonstrate that HIV-1 infection increases leukocyte adhesion and matrix metalloproteinase secretion. Clinical reports of AIDS patient's leukocyte integrin levels will also be reviewed and evidence that tissue localized HIV-1 infected cells could contribute to a variety of HIV-1 associated syndromes will be presented.     

X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution

We report the crystal structure of nucleoside diphosphate kinase (NDP kinase) from Dictyostelium discoideum with thymidine diphosphate (dTDP) and Mg2+ bound at the active site. The structure has been refined to an R-factor of 18.3% at 2-A resolution. The base stacks on the aromatic ring of Phe 64 near the protein surface and is wedged between the side chains of Phe 64 and Val 116. The sugar and the pyrophosphate are deeper inside the protein and make numerous H-bonds with protein side chains. There is no backbone interaction with the nucleotide. A Mg2+ ion bridges the alpha- and beta-phosphates and interacts with the protein via water molecules. NDP kinase shows little specificity toward ribonucleotides and deoxyribonucleotides. This property, required by the enzyme biological function, can now be analyzed by comparing the crystal structures of free, ADP-ligated, and dTDP-ligated enzymes. The most significant differences are located in residues 60-64, which adapt their conformation to allow Phe 64 to stack on both types of bases. Nonspecific binding is achieved by the absence of polar interaction between the base and protein atoms. The ribose of ADP and the deoxyribose of dTDP occupy similar positions, their hydroxyl groups interacting with Lys 16 and Asn 119. The H-bond between Lys 16 and the O2' hydroxyl of ADP is replaced by a similar interaction with a water molecule in the dTDP complex. The beta-phosphate position is the same for ADP and dTDP, suggesting that the mechanism of phosphate transfer is the same for all substrates ofNDP kinase.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ofuji's papulo-erythroderma: treatment with cyclosporin A

BACKGROUND: Papuloerythroderma of Ofuji is an uncommon condition characterized by diffuse pruriginous eruptions of infiltrating papulae. The large folds are not involved. The eruptions are associated with lymphopenia and eosinophilia. Very few cases have been reported in the literature and because of their heterogeneous nature, there is some debate as to whether this is a single clinical entity or a particular presentation of erythrodermia; Immunomodulation is recommended. CASE REPORT: A 73 year-old man of asian origin living in France presented chronic pruriginous erythrodermia with flat purplish-brown confluent papulae which did not involve the large folds. Eosophilia and lymphopenia were present. The biopsy specimen evidenced dermal infiltration with CD4+CD45+RO+ T cells, eosinophils and DC1a+ dendritic cells. Further explorations did not reveal any sign favoring lymphoma, carcinoma or underlying infection. Dermocorticoids, PUVA-therapy and interferon-alpha were ineffective. Considerable clinical improvement was obtained with cyclosporine A. DISCUSSION: We used ciclosporine A in our patient after repeated failure of other therapies reported to be effective in this dermatosis. Despite the favorable outcome, this therapeutic approach should be used with prudence.     

Long-term treatment of lupus nephritis with cyclosporin A

We evaluated the efficacy and safety of long-term treatment with cyclosporin A (CSA) in type IV lupus nephritis. Seventeen patients with biopsy-proven WHO type IV lupus nephritis were enrolled in a prospective, open study. Twelve of the 17 completed 48 months of treatment with CSA and prednisolone. Three patients required the addition of azathioprine, at 12, 38 and 47 months, respectively, for cutaneous disease flare with refractory rashes. One patient was lost to follow-up at 40 months. The mean +/- SD duration of treatment was 43.2 +/- 10.1 months (range 15.7-48 months). A significant reduction of proteinuria and a significant rise in serum albumin were noted 1 month after initiation of treatment. Improvement was maintained throughout the study except for three patients who relapsed with recurrence of nephrotic syndrome. There were no significant changes in serum creatinine level or creatinine clearances throughout the study. Repeat renal biopsy at 12 months following treatment with CSA showed histological improvement, with WHO type II changes in all 17 patients accompanying significant reduction in activity indices. Patients with baseline haemoglobin (Hgb) levels < 12 g/dl showed significant improvement. Serum C3 and C4 levels were not changed significantly. Corticosteroid-sparing effects were noted. Side-effects included hypertension, gum hypertrophy and mild hirsuitism, but were not serious. Combination therapy using CSA and prednisone is effective and safe for long-term treatment in lupus patients with WHO type IV nephritis.     

Interactions of cyclosporin A and amlodipine: blood cyclosporin A levels, hypertension and kidney function

The introduction of cyclosporin A has led to improved survival of allografts in humans. However, the use of cyclosporin A is associated with an increased prevalence of hypertension in kidney transplant recipients. Renal vasoconstriction and enhancement of tubular reabsorption contribute to this hypertensive effect. Concomitant treatment with calcium channel blockers blocks or ameliorates most of these adverse effects. This paper reviews the short-term effects of the calcium channel blocker amlodipine on plasma levels of cyclosporin A and its interaction with blood pressure and kidney function.     

Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP

Three previously described mutant Escherichia coli glutaminyl-tRNA synthetase (GlnRS) proteins that incorrectly aminoacylate the amber suppressor derived from tRNATyr (supF) with glutamine were cocrystallized with wild-type tRNAGln and their structures determined. In two of the mutant enzymes studied, Asp235, which contacts base pair G3-C70 in the acceptor stem, has been changed to asparagine in GlnRS7 and to glycine in GlnRS10. These mutations result in changed interactions between Asn235 of GlnRS7 and G3-C70 of the tRNA and an altered water structure between Gly235 of GlnRS10 and base pair G3-C70. These structures suggest how the mutant enzymes can show only small changes in their ability to aminoacylate wild-type cognate tRNA on the one hand and yet show a lack of discrimination against a noncognate U3-A70 base pair on the other. In contrast, the change of Ile129 to Thr in GlnRS15 causes virtually no change in the structure of the complex, and the explanation for its ability to misacylate supF is unclear.     

Life-table analysis of cyclosporin A treatment in psoriatic arthritis: comparison with other disease-modifying antirheumatic drugs

OBJECTIVES: The aim of this study was to determine the cumulative probability of taking CsA in comparison to other DMARDs, as well as the reason for discontinuation of each DMARD, in a large cohort of PsA patients. METHODS: We prospectively studied 172 consecutive patients with a diagnosis of PsA who had been admitted to our rheumatological unit since 1984. We collected information about treatment with DMARDs including: number, dose, duration and causes of withdrawal, including side effects or inefficacy. Cumulative survival analysis was performed by the Kaplan-Meier test and the differences between these survival curves were determined by the Mantel-Hanszel test. RESULTS: The probability curve of continuing to take CsA was significantly lower than that of MTX (p < 0.046). The rate of adverse effects responsible for stopping DMARD therapy was higher in the CsA group, especially with respect to the antimalarial group (p < 0.014). The most common cause of CsA withdrawal was hypertension. The rate of withdrawal due to inefficacy in the CsA group was not significantly different from those observed in the other groups. Nevertheless, the total frequency of discontinuation due to toxicity and inefficacy in the MTX group was significantly lower compared to the gold salts (p < 0.05) and CsA groups (p < 0.01). CONCLUSION: Life-table analysis suggests that PsA patients taking CsA are less likely than patients on MTX to continue long term treatment. Therefore CsA, which seems to be less safe than the antimalarials, could be considered a useful drug in the treatment of PsA, but does seem to represent the drug of first choice, particularly when compared to MTX.     

X-ray structures of new dipeptide taste ligands

AIMS/BACKGROUND: The mechanism of interaction and the role played by the vesicle lipid composition for the selective association between liposomes and liver cells were studied, at the ultrastructural level, by investigating both in situ and in vitro the interaction between hepatocytes, Kupffer and endothelial liver cells with egg-phosphatidylcholine (eggPC) or eggPC/stearylamine (9:1; mol:mol) reverse-phase evaporation (REV) liposomes. METHODS: Liver cells from rats, isolated by enzymatic perfusion and purified by differential centrifugation, were incubated, in a rotating bath at 37 degrees C, with liposomes (2.5 mM final liposomal lipid concentration). Cell aliquots were withdrawn and processed for electron microscope observation at fixed time intervals. Parallel experiments were carried out by in situ liver perfusion with liposome suspensions. RESULTS AND CONCLUSIONS: Our first conclusions are: 1) lipidic composition affects the rate of liposomes uptake and internalization by hepatocytes; 2) liposome uptake by hepatocytes or Kupffer cells is likely an endocytic process; 3) endothelial cells internalize lipid vesicles as well; 4) liposome uptake was due to a phagocytic activity for all isolated liver cells, while in the in situ observation endothelial cells seem to use another mechanism (fusion); and 5) the rate of internalization is related to the viability of the treated cells. Experimental data seem to indicate that differential behaviour in the internalization of lipid vesicles exists among parenchymal, Kupffer and endothelial liver cells. These differences suggest that clearance of liposomes by these cells involves two mechanisms (i.e., endocytosis or fusion) with different rates of uptake and internalization that facilitate the design of carriers that can deliver drugs preferentially to a specific liver cell type.     

Serum chemokines in patients with psoriatic arthritis treated with cyclosporin A

OBJECTIVE: To investigate the possible effects of neuropeptide Y on steroid release by human granulosa cells in culture. DESIGN: Prospective study. SETTING: A university laboratory and the division of obstetrics and gynecology in a hospital. PATIENT(S): Sixteen normally ovulating women. INTERVENTION(S): Ovulation induction for IVF-ET with an LH-releasing hormone analogue and gonadotropins. MAIN OUTCOME MEASURE(S): E2 and progesterone were assayed in the media conditioned by granulosa cells with the use of a double-antibody RIA. RESULT(S): Neuropeptide Y stimulates E2 production in a dose-dependent fashion. Preincubation for 3 hours with hCG led to a statistically significant increase in neuropeptide Y-induced E2 secretion. In contrast, whereas 3 hours of preincubation with 10(-7) mol/L of neuropeptide Y did not elicit a statistically significant increase in hCG-induced E2 secretion, coincubation for 48 hours significantly increased hCG-stimulated secretion. Unlike E2, progesterone secretion did not undergo any statistically significant or dose-dependent variation after treatment with neuropeptide Y. CONCLUSION(S): Neuropeptide Y plays a role in human ovarian steroidogenesis directly at the level of the granulosa cells of the follicles in the early stage of luteinization. In this way, neuropeptide Y could play an important role in controlling the positive feedback effect exerted by the ovarian steroids on LH-releasing hormone and gonadotropins in humans.     

Crystal structures of the inactive D30N mutant of feline immunodeficiency virus protease complexed with a substrate and an inhibitor

Crystal structures of complexes of a D30N mutant of feline immunodeficiency virus protease (FIV PR) complexed with a statine-based inhibitor (LP-149), as well as with a substrate based on a modification of this inhibitor (LP-149S), have been solved and refined at resolutions of 2.0 and 1.85 A, respectively. Both the inhibitor and the substrate are bound in the active site of the mutant protease in a similar mode, which also resembles the mode of binding of LP-149 to the native protease. The carbonyl oxygen of the scissile bond in the substrate is not hydrated and is located within the distance of a hydrogen bond to an amido nitrogen atom from one of the two asparagines in the active site of the enzyme. The nitrogen atom of the scissile bond is 3.25 A from the conserved water molecule (Wat301). A model of a tetrahedral intermediate bound to the active site of the native enzyme was built by considering the interactions observed in all three crystal structures of FIV PR. Molecular dynamics simulations of this model bound to native wild-type FIV PR were carried out, to investigate the final stages of the catalytic mechanism of aspartic proteases.     

Distribution analysis of the variation of B-factors of X-ray crystal structures; temperature and structural variations in lysozyme

The B-factor (isotropic temperature factor) data for X-ray structures of hen egg-white lysozyme from the study of Young et al. (Young, Dewan, Nave, and Tilton J. Appl. Cryst. 1993, 26, 309-319) potentially contain information about the relative contributions of static and dynamic variation to these factors. The six structures of the protein were obtained at two widely different temperatures (100 and 298 K), with two crystal forms (monoclinic and tetragonal) and other experimental differences. In addition, the monoclinic lysozyme crystals with two molecules per asymmetric unit allow direct examination of variation between structures determined under identical conditions at both temperatures. The B-factors from these structures all have complex distribution functions as might be expected considering all of the influences that these values must reflect. The empirical cumulative distribution functions (eCDF's) of these data show that they are representative of complex, multicomponent distributions. Distribution analysis using the DANFIP procedure (Wampler, Anal. Biochemistry 1990, 186, 209-218) of the data sets reveals that they can be modeled as four to six Gaussian subpopulations, that these subpopulations do not correlate with specific atom types, specific amino acid residues or fixed locations in the structure. While they do seem to correlate with localized groupings of atoms, these grouping vary from structure to structure even within the same crystal under the same conditions. Temperature seems to have a global effect in this case, but it is clear that other factors including experimental error influence the distribution of B-factors within a given structure. This analysis also helps explain the oft observed lack of atomic level correlation between experimental B-factors and calculated mean square displacements from molecular dynamics simulations.