Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics

The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine, Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments, The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in Delta C-p and positive values of both Delta Delta H degrees and aas of folding. Enthalpic effects were dominant, and the sign of Delta Delta S is the opposite of that expected from the hydrophobic effect. Values of Delta Delta G degrees and Delta Delta H degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.

Molecular phylogeny of Hemidactylus geckos (Squamata: Gekkonidae) of the Indian subcontinent reveals a unique Indian radiation and an Indian origin of Asian house geckos

Represented by approximately 85 species, Hemidactylus is one of the most diverse and widely distributed genera of reptiles in the world. In the Indian subcontinent, this genus is represented by 28 species out of which at least 13 are endemic to this region. Here, we report the phylogeny of the Indian Hemidactylus geckos based on mitochondrial and nuclear DNA markers sequenced from multiple individuals of widely distributed as well as endemic congeners of India. Results indicate that a majority of the species distributed in India form a distinct clade whose members are largely confined to the Indian subcontinent thus representing a unique Indian radiation. The remaining Hemidactylus geckos of India belong to two other geographical clades representing the Southeast Asian and West-Asian arid zone species. Additionally, the three widely distributed, commensal species (H. brookii, H. frenatus and H. flaviviridis) are nested within the Indian radiation suggesting their Indian origin. Dispersal-vicariance analysis also supports their Indian origin and subsequent dispersal out-of-India into West-Asian arid zone and Southeast Asia. Thus, Indian subcontinent has served as an important arena for diversification amongst the Hemidactylus geckos and in the evolution and spread of its commensal geckos. (C) 2010 Elsevier Inc. All rights reserved.

Estimating national contributions of greenhouse gas emissions :The CSE-WRI controversy

Analysts have identified four related questions that need to be asked and answered before agreements to respond to global warming will be possible.1 Which countries bear responsibility for causing the problem? What quantities and mix of greenhouse gases should each country be allowed to emit? Which countries have the resources to do something about the problem? Where are the best opportunities for undertaking projects to respond to the problem? Failure to distinguish among these four questions, or willingness to accept superficial answers, promotes unnecessary controversy.

Effect of packing density and adsorption parameters on the throughput of a thermal compressor

Vapour adsorption refrigeration systems (VAdS) have the advantage of scalability over a wide range of capacities ranging from a few watts to several kilowatts. In the first instance, the design of a system requires the characteristics of the adsorbate-adsorbent pair. Invariably, the void volume in the adsorbent reduces the throughput of the thermal compressor in a manner similar to the clearance volume in a reciprocating compressor. This paper presents a study of the activated carbon +HFC-134a (1,1,1,2-tetrafluoroethane) system as a possible pair for a typical refrigeration application. The aim of this study is to unfold the nexus between the adsorption parameters, achievable packing densities of charcoal and throughput of a thermal compressor. It is shown that for a thermal compressor, the adsorbent should not only have a high surface area, but should also be able to provide a high packing density. Given the adsorption characteristics of an adsorbent-adsorbate pair and the operating conditions, this paper discloses a method for the calculation of the minimum packing density necessary for an effective throughput of a thermal compressor. (C) 2002 Elsevier Science Ltd. All rights reserved.