The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Regional processes in mangrove ecosystems: spatial scaling relationships, biomass, and turnover rates following catastrophic disturbance

Physiological processes and local-scale structural dynamics of mangroves are relatively well studied. Regional-scale processes, however, are not as well understood. Here we provide long-term data on trends in structure and forest turnover at a large scale, following hurricane damage in mangrove ecosystems of South Florida, U.S.A. Twelve mangrove vegetation plots were monitored at periodic intervals, between October 1992 and March 2005. Mangrove forests of this region are defined by a −1.5 scaling relationship between mean stem diameter and stem density, mirroring self-thinning theory for mono-specific stands. This relationship is reflected in tree size frequency scaling exponents which, through time, have exhibited trends toward a community average that is indicative of full spatial resource utilization. These trends, together with an asymptotic standing biomass accumulation, indicate that coastal mangrove ecosystems do adhere to size-structured organizing principles as described for upland tree communities. Regenerative dynamics are different between areas inside and outside of the primary wind-path of Hurricane Andrew which occurred in 1992. Forest dynamic turnover rates, however, are steady through time. This suggests that ecological, more-so than structural factors, control forest productivity. In agreement, the relative mean rate of biomass growth exhibits an inverse relationship with the seasonal range of porewater salinities. The ecosystem average in forest scaling relationships may provide a useful investigative tool of mangrove community biomass relationships, as well as offer a robust indicator of general ecosystem health for use in mangrove forest ecosystem management and restoration.

Toward a unified theory of task -oriented and relationship -oriented leader behavior: A multi -country generalizability study

The theoretical foundation of this study comes from the significant recurrence throughout the leadership literature of two distinct behaviors, task orientation and relationship orientation. Task orientation and relationship orientation are assumed to be generic behaviors, which are universally observed and applied in organizations, even though they may be uniquely enacted in organizations across cultures. The lack of empirical evidence supporting these assumptions provided the impetus to hypothetically develop and empirically confirm the universal application of task orientation and relationship orientation and the generalizability of their measurement in a cross-cultural setting. Task orientation and relationship orientation are operationalized through consideration and initiation of structure, two well-established theoretical leadership constructs. Multiple-group mean and covariance structures (MACS) analyses are used to simultaneously validate the generalizability of the two hypothesized constructs across the 12 cultural groups and to assess whether the similarities and differences discovered are measurement and scaling artifacts or reflect true cross-cultural differences. The data were collected by the author and others as part of a larger international research project. The data are comprised of 2341 managers from 12 countries/regions. The results provide compelling evidence that task orientation and relationship orientation, reliably and validly operationalized through consideration and initiation of structure, are generalizable across the countries/regions sampled. But the results also reveal significant differences in the perception of these behaviors, suggesting that some aspects of task orientation and relationship orientation are strongly affected by cultural influences. These (similarities and) differences reflect directly interpretable, error-free effects among the constructs at the behavioral level. Thus, task orientation and relationship orientation can demonstrate different relations among cultures, yet still be defined equivalently across the 11 cultures studied. The differences found in this study are true differences and may contain information about cultural influences characterizing each cultural context (i.e. group). The nature of such influences should be examined before the results can be meaningfully interpreted. To examine the effects of cultural characteristics on the constructs, additional hypotheses on the constructs' latent parameters can be tested across groups. Construct-level tests are illustrated in hypothetical examples in light of the study's results. The study contributes significantly to the theoretical understanding of the nature and generalizability of psychological constructs. The theoretical and practical implications of embedding context into a unified theory of task orientated and relationship oriented leader behavior are proposed. Limitations and contributions are also discussed. ^