Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition

A theory of equilibrium denaturation of proteins is suggested. According to this theory, a cornerstone of protein denaturation is disruption of tight packing of side chains in protein core. Investigation of this disruption is the object of this paper. It is shown that this disruption is an "all-or-none" transition (independent of how compact is the denatured state of a protein and independent of the protein-solvent interactions) because expansion of a globule must exceed some threshold to release rotational isomerization of side chains. Smaller expansion cannot produce entropy compensation of nonbonded energy loss; this is the origin of a free-energy barrier (transition state) between the native and denatured states. The density of the transition state is so high that the solvent cannot penetrate into protein in this state. The results obtained in this paper make it possible to present in the following paper a general phase diagram of protein molecule in solution.     

Even if the fetus is not a person,abortion is immoral: The impairment argument

Much of the debate about the ethics of abortion has centered on whether the fetus is a person. In an attempt to sidestep this complex issue, I argue that, even if the fetus is not a person, abortion is immoral. To arrive at this conclusion, I argue that giving a fetus fetal alcohol syndrome is immoral, and that if this is so, then killing the fetus is immoral. Roughly, this is because killing the fetus impairs it more than giving it fetal alcohol syndrome. Since abortion (in most cases) amounts to killing the fetus, this means that abortion (in most cases) is immoral. I defend the premises of this argument against a plethora of objections, concluding that they either do not work, or commit their proponent to a controversial position.     

Components and mechanisms of thermal hyperpnea.

The pattern of breathing during a hyperthermia-induced hyperventilation varies across different species. Thermal tachypnea is a first phase panting response adopted during hyperthermia when tidal volume is minimized and the frequency of breathing is maximized. Blood-gas tensions and pH are maintained during this hyperventilation, and the associated heat loss helps the animal regulate its body temperature. A second pattern of breathing adopted in hyperthermia is thermal hyperpnea; this response is the focus of this review. This form of hyperventilation is evident after an increase in core temperature and it is apparent in humans. Increases of tidal volume as well as frequency of breathing are evident during this response that results in a respiratory alkalosis. The cause of thermal hyperpnea is not resolved; evidence of the potential mechanisms underlying this response support that modulators of the response act in either a multiplicative or additive manner with body temperatures. The details of the designs and methodologies of the studies supporting or refuting these two views are discussed. A physiological rationale for thermal hyperpnea is presented in which it is suggested this response serves a heat-loss role and contributes to selective brain cooling in hyperthermic humans. Ongoing research in this area is focused on resolving the mechanisms underlying thermal hyperpnea and its contribution to cranial thermoregulation. The direct application of this research is for the care of febrile and hyperthermic patients.     

1-Methyladenine in urine of an adenosine deaminase-deficient adult without immunodeficiency

Procedures are described for the isolation and identification of 1-methyladenine from the urine of an adult female with adenosine deaminase deficiency but no immunodeficiency. Evidence is provided indicating that much of the usual urinary excretion product, 1-methyladenosine, is converted to 1-methyladenine in this subject prior to excretion. Since the nucleoside phosphorylases present in normal individuals do not act on 1-methyladenosine, this suggests that a phosphorylase with unusual properties is present in this adenosine deaminase-deficient subject. A possible role for this phosphorylase in removal of deoxyadenosine in this subject is discussed.     

The relationship between the stiffness and the mineral content of bone

The modulus of elasticity (E) of bone increases very rapidly with increase in mineral content, and in this is atypical of most composite materials. It is proposed that this apparent anomaly is caused by the end-to-end fusion of apatite crystals as the matrix becomes saturated with mineral. There is electron microscopic evidence that this occurs. Calculations using a fairly simple model show that this mechanism could be effective in life.     

Stages of life: A new metaphysics of conceptionism

When a human being comes into existence is crucial in bioethics. Conceptionism is the view that a human being comes into existence at conception. The twinning argument is an influential objection to this view. All versions of the twinning argument rely on a metaphysics of material objects, namely, endurantism. Given this, a strategy for defending conceptionism against the twinning argument is to deny endurantism and adopt an alternative metaphysics of material objects. A version of this strategy which has been debated in this journal is to adopt perdurantism, or the ‘multiple occupancy view’, on which monozygotic twins share the zygote region as a temporal part. We present a novel version of this strategy: conceptionists can evade the twinning argument by adopting an exdurantist metaphysics of material objects. We suggest reasons for thinking that this is a plausible and, indeed, preferable way for conceptionists to avoid the twinning argument.     

Experience of an interactive program in undergraduate investigative practicals

A microcomputer program is described which has been used by first-year undergraduates throughout an investigation in microbiology, totalling five hours of practical work. The computer is used by students to check their suggestions of possible lines of investigation, the results of practical procedures, and the decisions made on the basis of this experimental evidence. The program offers advice when entries which are inadvisable or incorrect are entered thus providing guidance without usurping student control of the investigation. Evidence for the effectiveness of this program is presented and the potential for this type of consultative program in other areas is indicated. Based on this experience, advice is offered on the general design of this type of program.     

AP-1/jun binding sites mediate serum inducibility of the human vimentin promoter.

The vimentin gene is inducible by serum in quiescent Balb/c 3T3 cells, but the molecular mechanism of this induction is unknown. The results presented here represent a first step towards the elucidation of the pathway of events leading from growth factor-receptor interaction to this induction. A series of Bal 31 deletions of the human vimentin promoter are used to show that a sequence residing at -700 is responsible for the serum, and also TPA inducibility of this gene. This sequence is able to confer serum inducibility upon uninducible constructs regardless of its position and orientation, indicating that it is this element alone which is required for this induction. The isolated sequence is a strong enhancer as well. Further deletions and the use of synthetic oligonucleotides demonstrate that a 24-mer containing two AP-1/jun binding sites confer both serum and TPA inducibility upon the human vimentin gene. Gel retardation analysis confirms that this sequence binds an AP-1 -like protein.     

Splicing and transport of eukaryotic mRNAs: a theoretical model

Several years have already elapsed since the first discovery of splicing in eukaryotic mRNAs. In this process sections of the precursor mRNAs are spliced out (these are named introns) and the two remaining excised sites, 5′ and 3′ are ligated to form the mature mRNA chains.Very little is known about the splicing and ligation mechanism or about its location inside the cell. It is known to take place in the nucleus, but it is unknown whether it occurs inside the nuclear matter or on the surface of its membrane. Since nearly all eukaryotic messengers undergo splicing, this is a central question.From the theoretical point of view this is an intriguing problem. A lot of data have recently accumulated which have a bearing on this question. Based on current knowledge, this paper proposes a model in which splicing is carried out on the surface of the nuclear membrane and in concert with transport across it. It is suggested that the enzymes that take part in this process are loosely associated with the membrane pore complex. Evidence and results which are relevant to this question are given and discussed.     

Parasite prevalence and host sample size

Parasite prevalence is a summary statistic familiar to biologists. However, that there is an interspecific relationship between prevalence and sample size (the number of host individuals examined for parasites) is not widely appreciated. In this article, Richard Gregory and Tim Blackburn present some examples of this negative relationship, explain the mechanisms that underlie this pattern and discuss the potential problems this association might create for biological studies.     

Force enhancement following an active stretch in skeletal muscle

When skeletal muscle is stretched during a tetanic contraction, the resulting force is greater than the purely isometric force obtained at the corresponding final length. Several mechanisms have been proposed to explain this phenomenon, but the most accepted mechanism is the sarcomere length non-uniformity theory. This theory is associated with the notion of instability of sarcomeres on the descending limb of the force–length relationship. However, recent evidence suggests that this theory cannot account solely for the stretch-induced force enhancement. Some of this evidence is presented in this paper, and a new mechanism for force enhancement is proposed: one that is associated with the engagement of a passive force during stretch. We speculate that this passive force enhancement may be caused by titin, a protein associated with passive force production at long sarcomere lengths.     

Frequency-dependent diffraction from enzymatic breathing modes.

The intensity of the time-dependent Fourier transform of any macro-molecule which contains a cleft of the sort that exists in the protein lysozyme is derived. It is shown that there is a region of this transform in which this intensity varies nearly sinusoidally with time with a frequency equal to that of the macromolecule's breathing mode of vibration, and where, therefore, the diffracted power will be primarily at this single frequency. Observation of this power will allow the experimental determination of the frequency of this mode, which is expected to be much lower than those observable by Raman spectroscopy.     

On the 'rate of aging' in heterogeneous populations

It is well known that the rate of aging is constant for populations described by the Gompertz law of mortality. However, this is true only when a population is homogeneous. In this note, we consider the multiplicative frailty model with the baseline distribution that follows the Gompertz law and study the impact of heterogeneity on the rate of aging in this population. We show that the rate of aging in this case is a function of age and that it increases in (calendar) time when the baseline mortality rate decreases.     

Establishment of the primary imprint of the HYMAI/PLAGL1 imprint control region during oogenesis

Imprinting within domains occurs through epigenetic alterations to imprinting centers (ICs) that result in the establishment of parental-specific differences in gene expression. One candidate IC lies within the imprinted domain on human chromosome region 6q24. This domain contains two paternally expressed genes, the zinc finger protein gene PLAGL1 (ZAC/LOT1) and an untranslated mRNAcalled HYMAI. The putative IC overlaps exon 1 of HYMAI and is differentially methylated in somatic tissues. In humans, loss of methylation within this region is seen in some patients with transient neonatal diabetes mellitus, and hypermethylation of this region is found in ovarian cancer and is associated with changes in expression of PLAGL1, suggesting that it plays a key role in regulating gene expression. Differential methylation within this region is conserved in the homologous region on mouse chromosome 10A and is present on the maternal allele. In this paper, we report that DNA methylation is established during the growth phase of oogenesis and that this coincides with the establishment of monoallelic expression from this region lending further support to the hypothesis that this region functions as an IC.     

Comment

Conclusion  In such a situation the only approach possible, even for a prospective LCA study, is to aggregate data from the possible sources of delivery and to use this as an input to the study. Weidema states in his article that actual average data is more difficult to collect than data for a marginal situation. But this is no argument against using average data when this is what most correctly portrays the actual situation. We would argue that this is also the only correct approach for a global commodity, since this will be the real situation for any new product. The material going into it will potentially be an average of the existing material on the market.     

Maintenance of Asymmetric Cellular Localization of an Auxin Transport Protein through Interaction with the Actin Cytoskeleton

In shoots, polar auxin transport is basipetal (that is, from the shoot apex toward the base) and is driven by the basal localization of the auxin efflux carrier complex. The focus of this article is to summarize the experiments that have examined how the asymmetric distribution of this protein complex is controlled and the significance of this polar distribution. Experimental evidence suggests that asymmetries in the auxin efflux carrier may be established through localized secretion of Golgi vesicles, whereas an attachment of a subunit of the efflux carrier to the actin cytoskeleton may maintain this localization. In addition, the idea that this localization of the efflux carrier may control both the polarity of auxin movement and more globally regulate developmental polarity is explored. Finally, evidence indicating that the gravity vector controls auxin transport polarity is summarized and possible mechanisms for the environmentally induced changes in auxin transport polarity are discussed.     

Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding

AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis in mammals. AMP is believed to control the activity of AMPK by binding to the gamma subunit of this heterotrimeric enzyme. This subunit contains two Bateman domains, each of which is composed of a tandem pair of cystathionine beta-synthase (CBS) motifs. No structural information is currently available on this subunit, and the molecular basis for its interactions with AMP is not well understood. We report here the crystal structure at 1.9 Angstrom resolution of the Bateman2 domain of Snf4, the gamma subunit of the yeast ortholog of AMPK. The structure revealed a dimer of the Bateman2 domain, and this dimerization is supported by our light-scattering, mutagenesis, and biochemical studies. There is a prominent pocket at the center of this dimer, and most of the disease-causing mutations are located in or near this pocket.     

Price of disorder in the lac repressor hinge helix

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.     

Rhythmicity of Flowering in Pharbitis nil

When young seedlings of Pharbitis nil are grown under continuous light, except for a single inductive dark period, they flower to a varying degree, depending on when this dark period is given. Plants become sensitive to this induction approximately three days after the seedlings emerge from the soil. The expression of flowering varies in a rhythmic fashion for three or more cycles, when an inductive dark period is given at progressively later times. The time between maximum expression of flowering is 24 hours or somewhat longer. It appears necessary that the inductive dark period be of sufficient duration, to only partially induce the plants to flower for this rhythm to be expressed. Under the conditions employed in this study, this duration is 12 hours. If this rhythm is endogenous, it exists at least from when the plants emerged from the soil since no environmental cues are given after that time, and it raises questions of the interpretations of data from previous studies with this organism.     

The control of sexual identity in the Drosophila germline

Whether to be male or female is a critical decision in development. Nowhere is this more important than in the germ cells, which must produce either the sperm or eggs necessary for the perpetuation of the species. How does a germ cell make this decision and how is it executed? One thing that is clear is that this process is very different in germ cells compared with other cells of the embryo. Here, we explore how sexual identity is established in the Drosophila germline, how this affects other aspects of germ cell development and what studies in Drosophila can teach us about mammalian germ cells.