Entropic stabilization of proteins and its proteomic consequences

We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in folded states of proteins. This finding suggests that Lysines would preferentially entropically stabilize the native state. Indeed we show in computational experiments that Arginine-to-Lysine amino acid substitutions result in noticeable stabilization of proteins. We then hypothesize that if evolution uses this physical mechanisms in its strategies of thermophilic adaptation then hyperthermostable organisms would have much greater content of Lysines in their proteomes than of comparable in size and similarly charged Arginines.. Consistent with that, high-throughput comparative analysis of complete proteomes shows extremely strong bias towards Arginine-to-Lysine replacement in hyperthermophilic organisms and overall much greater content of Lysines than Arginines in hyperthermophiles. This finding cannot be explained by GC compositional biases. Our study provides an example of how analysis of a delicate physical mechanism of thermostability helps to resolve a puzzle in comparative genomics as to why aminoacid compositions of hyperthermophilic proteomes are significantly biased towards Lysines but not Arginine

Dealing with urban terror: heritages of control, varieties of intervention, strategies of research

The events of September 11th bring urgency to problems of urban security, both in terms of finding ways to protect cities from attacks by terrorists and also protecting urban life from repressive measures that form in reaction to those attacks. We outline a rationale for urbanists to participate in analysis and policy-formulation on security issues and examine the utility of past urban research strategies, including criminology, in terms of their relevance to the current challenge. We suggest principles to guide future urban policy in light of past experiences. Copyright Joint Editors and Blackwell Publishing Ltd 2003.