Polarity as a criterion in protein design

Hypothetical proteins can be tested computationally by determining whether or not the designed sequence-structure pair has the characteristics of a typical globular protein. We have developed such a test by deriving quantities with approximately constant value for all globular proteins, based on empirical analysis of the exposed and buried surfaces of 128 structurally known proteins. The characteristic quantities that best appear to segregate badly designed or deliberately misfolded proteins from their properly folded natural relatives are the polar fraction of side chains on the protein surface and, independently, in the protein interior. Three of the seven hypothetical structures tested here can be rejected as having too many polar side-chain groups in the interior or too few on the protein surface. In addition, a recently designed nutritional protein is identified as being very much unlike globular proteins. These database-derived characteristic quantities are useful in screening designed proteins prior to experiment and may be useful in screening experimentally determined (X-ray, NMR) protein structures for possible errors.     

Crystal structure of thermitase from Thermoactinomyces vulgaris at 2.2 A resolution

The crystal structure of thermitase from Thermoactinomyces vulgaris has been determined by x-ray diffraction at 2.2 A resolution. The structure was solved by a combination of single isomorphous replacement and molecular replacement methods. The structure was refined to a conventional R factor of 0.24 using restrained least square procedures CORELS and PROLSQ. The tertiary structure of thermitase is similar to that of subtilsin BPN'. The greatest differences between these structures are related to the insertions and deletions in the sequence.     

An estimate on the effect of point mutation and natural selection on the rate of amino acid replacement in proteins

We outline a method for estimating quantitatively the influence of point mutations and selection on the frequencies of codons and amino acids. We show how the mutation rate, i.e., the rate of amino acid replacement due to point mutation, can be affected by the codon usage as well as by the rates of the involved base exchanges. A comparison of the mutation rates calculated from reliable values of codon usage and base exchange probabilities with those that would be expected on the basis of chance reveals a notable suppression of replacements leading to tryptophan, glutamate, lysine, and methionine, and particularly of those leading to the termination codons. If selection constraints are neglected and only mutations are taken into account, the best agreement between expected and observed frequencies of both codons and amino acids is obtained for alpha = 1.13-1.15, where (Formula: see text). The "selection values" of codons and amino acids derived by our method show a pattern that partially deviates from others in the literature. For example, the selection pressure on methionine and cysteine turns out to be much more pronounced than expected if only the discrepancies between their observed and expected occurrences in proteins are considered. To estimate to what extent randomly occurring amino acid replacements are accepted by selection, we constructed an "acceptability matrix" from the well-established matrix of accepted point mutations. On the basis of this matrix "acceptability values" of the amino acids can be defined that correlate with their selection values. We also examine the significance of mutations and selection of amino acids with respect to their physicochemical properties and functions in proteins. The conservatism of amino acid replacements with respect to certain properties such as polarity can be brought about by the mutational process alone, whereas the conservatism with respect to other relevant properties--among them all measures of bulkiness--obviously is the result of additional selectional constraints on the evolution of protein structures.     

Zur Feinstruktur von Cuticula und Epidermis beim Flußkrebs Orconectes limosus während eines Häutungszyklus

Zusammenfassung Die Cuticula an der Innen- und Außenseite der Branchiostegite des Flußkrebses besteht wie für Arthropoden üblich aus Epi- und Procuticula. Sowohl die Epicuticula als auch die Procuticula von Innen- und Außenseite unterscheiden sich im Feinbau wesentlich voneinander. An der Innenseite ist die Epicuticula einfach gebaut; Die Procuticula ist lamelliert und zeigt meist die bogenförmigen Muster von Mikrofibrillen. Die Epicuticula an der Außenseite weist in den in dieser Arbeit untersuchten Entwicklungsstadien einen sehr viel komplizierteren Feinbau auf, der in der Entwicklung gewissen Änderungen unterliegt. In der wiederum lamellierten Procuticula an der Außenseite sind die Mikrofibrillen zu Balken gebündelt. Die Ausrichtung der Mikrofibrillen dreht sich innerhalb einer Lamelle um 180°. Durch die Procuticula ziehen Fortsätze der Epidermiszellen, außerdem Stäbe der sog. Verbindungsstrukturen.Die Bildung der Cuticula an der Innenseite konnte weitgehend vollständig verfolgt werden; sie ist gut mit der Bildung der Cuticula bei verschiedenen Insekten vergleichbar.Die Bildung der Cuticula an der Außenseite konnte dagegen nur von Beginn der Abscheidung der Proouticula bis zur Häutung verfolgt werden. Kurz vor Beginn der Cuticulaabscheidung kommt es in den Epidermiszellen zu einer stärkeren Entwicklung des rauhen ER. Während der gesamten von uns verfolgten Bildungsstadien sieht man Vesikel mit dichtem Inhalt besonders in der Nähe des Zellapex. Sie geben anscheinend hier ihren Inhalt, Cuticulamaterial, nach außen ab. Sie stammen wohl aus Golgibereichen. Auch Stachelsaumbläschen (coated vesicles) kommen regelmäßig vor, deren genetischer Zusammenhang mit multivesikulären Körpern diskutiert wird. Bei der Abscheidung der fibrillären Cuticulasubstanzen spielen besondere Differenzierungen der Zell oberfläche, — kappenartige Verdichtungen der Zelloberfläche, meist an der Spitze kleiner Mikrovilli — eine wesentliche Rolle.

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The ultrastructure of cuticle and epidermis in the crayfish Crconectes limosus during a moulting cycle

Summary The cuticle of the inside and outside of the branchiostegites of the crayfish consists of an epicuticle and a procuticle — as common in arthropods. Concerning their ultrastructure epicuticle and procuticle differ essentially from each other on both the inside as well as the outside. On the inside the epicuticle is built plainly; the procuticle is laminated, and, mostly it shows the arched patterns of microfibrils. In those developmental stages investigated in this project the epicuticle of the outside shows a much more intricated ultrastructure, since during formation it is subject to certain changes. On the outside the procuticle is also laminated; the microfibrils are bundled up to bars. The alignment of those microfibrils within one lamella is twisted for 180°. The procuticle is penetrated by processes of epidermal cells and by rods of the so-called connecting structures.The formation of the cuticle on the inside was observed completely; it is comparable to the forming of the cuticle in several insects. However, the formation of the cuticle on the outside was only observed from the beginning of the procuticular development up to the moulting.Shortly before formation of the cuticle the development of rough ER in the epidermal cells seems to be intensified. In all of developmental stages observed there appear vesicles with dense contents mainly situated nearby the cell apex. At this site they evidently deliver their contents — cuticular materials — to the outside of the cell; they probably originate in the Golgi areas. There occur coated vesicles regularity, too; their genetic relation to multivesicular bodies is discussed. Special differentiation on the cell surface i.e. dome-like consolidations of the cell surface mainly placed at the tip of small microvilli are of great importance for the secretion of the cuticle substances.

     

Crystal structure of thermitase and stability of subtilisins

Crystal structure of thermitase, a serine proteinase from Thermoactinomyces vulgaris, has been determined by X-ray diffraction at 1.4 A resolution. The atomic model of thermitase refined to an R-factor of 0.149 contains 1997 protein atoms, 182 water molecules and 2 Ca2+ ions. The tertiary structure of thermitase is similar to that of subtilisin BPN'. The greatest variations are connected with insertions and deletions in the amino acid sequence, which are located on the surface of the molecule. Higher thermostability of thermitase can be explained in terms of the three-dimensional structure. The Ca2+ ions, bound to the protein molecule, as well as the ionic and hydrophobic interactions are supposed to give the main contribution to the stabilization of the structure.     

Effect of organic matter on growth and cell yield of ammonia-oxidizing bacteria

The effect of various organic compounds on the growth of ammonia-oxidizing bacteria was examined.Nitrosococcus oceanus, a strongly halophilic bacterium, had a very low tolerance to organic matter compared with other organisms tested. Organic compounds scarcely affected the growth of theNitrosomonas strains whereas nitrite formation by bothNitrosococcus mobilis strains was inhibited by nearly all of the substances tested. The growth ofNitrosospira strain Nsp₁ was enhanced more than 30% by acetate and formate, but not growth was detectable in the presence of pyruvate. On the contrary,Nitrosospira strain Nsp₅ was stimulated only by pyruvate. Nitrite formation by the twoNitrosovibrio tenuis strains tested was similar. The growth of both strains was enhanced considerably by formate and glucose; acetate and, to a greater extent, pyruvate inhibited these bacteria.In batch culture, the energy efficiency of autotrophically grown ammonia-oxidizing bacteria varied from strain to strain. The cell yield of mixotrophically grown cultures, per unit of ammonia oxidized, was increased in comparison with autotrophic ones. No heterotrophic growth was detected.     

Citrate lyase from Streptococcus diacetilactis

Citrate lyase (EC 4.1.3.6) was purified 38-fold from cell-free extracts of Streptococcus diacetilactis. The enzyme was homogeneous in analytical ultracentrifugation and polyacrylamide gel electrophoresis The final enzyme preparation contained acetate: HS-citrate lyase ligase—an acetylating enzyme which converts inactive HS-citrate lyase into enzymatically active acetyl-S-citrate lyase. This enzyme activity was purified 25-fold over the crude extract and seemed to be associated with citrate lyase. Partially purified citrate lyase from Leuconostoc citrovorum contained also its acetylating enzyme. Purified citrate lyases from Klebsiella aerogenes and Rhodopseudomonas gelatinosa were devoid of acetylating enzyme activity. The HS-form of citrate lyase from S. diacetilactis was completely acetylated and hence activated by incubation with ATP and acetate for 25 min at 25° C. The enzyme did not acetylate the HS-lyases from R. gelatinosa and K. aerogenes. In contrast to the citrate lyases from R. gelatinosa and K. aerogenes the enzymes from S. diacetilactis and L. citrovorum showed onlya very weak reaction inactivation. It is assumed that this is due to the association of the acetylating enzymes with these lyases.     

A muscle controlled finite-element model of laryngeal abduction and adduction

A three-dimensional finite-element model was developed to simulate the complex movement of the laryngeal cartilages during vocal fold abduction and adduction. The model consists of cricoid and arytenoid cartilages, as well as the intralaryngeal muscles and vocal folds. The active and passive properties of the muscles were idealised by one-dimensional elements based on the Hill theory. Its controlling input value is a time dependent stimulation rate. Optimisation loops have been carried out for the arrangement of the individual stimulation rates. Since in vivo measurements are not feasible, the developed biomechanical model shall be used to analyse the force distribution within the laryngeal muscles during phonatory manoeuvres. Simulations of abduction and adduction in different pitches of voice lead to realistic tensions of the vocal folds. The model is a first step to analyse motional vocal fold diseases and to predict the consequences of phonosurgical interventions.     

Role of serum concentration of VEGFR1 and TIMP2 on clinical outcome in primary cervical cancer: Results of a companion protocol of the randomized,NOGGO–AGO phase III adjuvant trial of simultaneous cisplatin-based radiochemotherapy vs. carboplatin and paclitaxel containing sequential radiotherapy

ObjectiveAim of the present study was to analyze the expression-profile of IGF1, IGFBP3, sICAM1, sVCAM1, MMP2, MMP9, TIMP2, VEGFA, VEGFD, VEGFC and VEGFR1 in patients with high-risk FIGO-stage Ib-IIb cervical cancer.MethodsSerum from 68 cervical cancer patients treated within a phase-III-trial with either simultaneous cisplatin radiochemotherapy or sequential systemic carboplatin and paclitaxel followed by percutaneous irradiation was analyzed by ELISA. Both target expression and correlation with important clinicopathological factors were analyzed following standard statistic procedures.ResultsAll 68 patients underwent a primary radical hysterectomy with pelvic and/or paraaortic lymphadenectomy. 85.3% of the extirpated tumors had clear surgical margins (R0). Increased levels of VEGFR1, TIMP2 and MMP2 were significantly associated with positive surgical margins (p = 0.004, p = 0.018 and p = 0.004, respectively). High concentration of MMP2 and TIMP2 correlated additionally with an advanced age at time of diagnosis (p = 0.001 and p = 0.007, respectively). For the cut-off value of 100 pg/ml, an increased VEGFR1 was significantly associated with poor overall (OS) and progression-free (PFS) survival (p = 0.017 and p = 0.015, respectively). A TIMP2 concentration of lower than 90 ng/ml was significantly associated with poorer OS and PFS (p = 0.009 and p = 0.043, respectively). In the multivariate analysis, TIMP2 expression in serum was the only independent prognostic factor for OS (p = 0.032, HR = 6.51, 95% CI = 1.17–36.01).ConclusionsExpression-profile of specific biomarkers associated with tumor invasion, cell migration and angiogenesis seems to be of prognostic value for both OS and PFS in patients undergoing surgery due to primary cervical cancer. Further analyses are warranted to allow an implementation of such markers into clinical practice.