BackgroundToday, recognition and classification of sequence motifs and protein folds is a mature field, thanks to the availability of numerous comprehensive and easy to use software packages and web-based services. Recognition of structural motifs, by comparison, is less well developed and much less frequently used, possibly due to a lack of easily accessible and easy to use software.ResultsIn this paper, we describe an extension of DeepView/Swiss-PdbViewer through which structural motifs may be defined and searched for in large protein structure databases, and we show that common structural motifs involved in stabilizing protein folds are present in evolutionarily and structurally unrelated proteins, also in deeply buried locations which are not obviously related to protein function.ConclusionsThe possibility to define custom motifs and search for their occurrence in other proteins permits the identification of recurrent arrangements of residues that could have structural implications. The possibility to do so without having to maintain a complex software/hardware installation on site brings this technology to experts and non-experts alike.

We have determined the solution structure of an albumin binding domain of protein G, a surface protein of group C and G streptococci. We find that it folds into a left handed three-helix bundle similar to the albumin binding domain of protein PAB from Peptostreptococcus magnus. The two domains share 59% sequence identity, are thermally very stable, and bind to the same site on human serum albumin. The albumin binding site, the first determined for this structural motif known as the GA module, comprises residues spanning the first loop to the beginning of the third helix and includes the most conserved region of GA modules. The two GA modules have different affinities for albumin from different species, and their albumin binding patterns correspond directly to the host specificity of C/G streptococci and P. magnus, respectively. These studies of the evolution, structure, and binding properties of the GA module emphasize the power of bacterial adaptation and underline ecological and medical problems connected with the use of antibiotics.In the complex molecular interplay between a pathogen and its human host, protein-protein interactions play important roles. For instance, bacteria express surface proteins that interact with abundant human extracellular proteins with high affinity and specificity. In human plasma, albumin (HSA) 1 and immunoglobulins (Ig) are the quantitatively dominating proteins, and significant human pathogens have developed surface proteins that bind these and other plasma proteins (for references, see Ref 1). Two of the most well known such proteins are protein A of Staphylococcus aureus (2) and protein G of group C and G streptococci (3, 4), which both bind to the Fc region of IgG. In 1980, Myhre and Kronvall (5) reported that HSA could bind to the surface of various streptococcal species, including group C and G streptococci. It was later found that protein G was responsible also for the interaction with HSA (6). Protein G has separate binding domains for IgG and HSA (7,8), and as a result C and G streptococci are in vivo covered with an inner layer of IgG and an outer layer of HSA. Peptostreptococcus magnus are strictly anaerobic bacteria that are part of the indigenous human flora of the skin, oral cavity, and gastrointestinal and urogenital tracts. Some isolates of this species bind HSA (9), and notably these isolates are mostly from patients with deep wound infections (10), suggesting that HSA binding turns the commensal P. magnus into a potential pathogen. The surface protein of P. magnus binding HSA is called PAB, and it contains a domain of 45 residues showing a high degree of sequence homology with the HSA binding domains of protein G (11). Analysis of the gene encoding PAB suggested that this domain originates from protein G and has been transferred to and introduced into the pab gene through the action of a conjugational plasmid (related to pCF10 of Enterococcus faecalis) followed by a recombinational event (11). This interspecies exchange of a structurally well defined motif repre...

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ABSTRACT. Fire has long been a principal tool for manipulating ecosystems, notably for pastoralist cultures, but in modern times, fire use has often been a source of conflicts with state bureaucracies. Despite this, traditional fire management practices have rarely been examined from a perspective of fire behavior and fire effects, which hampers dialogue on management options. In order to analyze the rationale for fire use, its practical handling, and ecological effects in high-elevation ericaceous heathlands in Ethiopia, we used three different information sources: interviews with pastoralists, field observations of fires, and analysis of vegetation age structure at the landscape level. The interviews revealed three primary reasons for burning: increasing the grazing value, controlling a toxic caterpillar, and reducing predator attacks. Informants were well aware of critical factors governing fire behavior, such as slope, wind, vertical and horizontal fuel structure, and fuel moisture. Recent burns (1-4 years since fire) were used as firebreaks to control the size of individual burns, which resulted in a mosaic of vegetation of different ages. The age structure indicated an average fire return interval of ~10 years. At these elevations (> 3500 m), the dry period is unreliable, with occasional rains. Of all observed fires, 83% were ignited during very high Fire Weather Index levels, reached during only 11% of all days of the year. Burning is illegal, but if this ban was respected, our data suggest that the Erica shrubs would grow out of reach of cattle within a few years only, creating a dense and continuous canopy. This would also create a risk of large high-intensity wildfires since the landscape is virtually devoid of natural fuel breaks. Under the present management regime, this heathland ecosystem should be quite resilient to degradation by fire due to a relatively slow fuel buildup (limiting fire intervals) and an effective regrowth of Erica shoots. Nevertheless, if burning is done during severe drought, there may be a risk of smoldering fires killing the lignotubers. Given the intimate knowledge of fire behavior and fire effects among these pastoralists, it should be possible to develop a fire management plan that can sustain the present land use and ecosystem, and be sanctioned by both authorities and the local community.

Fire is the most frequent disturbance in the Ericaceous Belt ( ca 3000–4300 m.a.s.l.), one of the most important plant communities of tropical African mountains. Through resprouting after fire, Erica establishes a positive fire feedback under certain burning regimes. However, present-day human activity in the Bale Mountains of Ethiopia includes fire and grazing systems that may have a negative impact on the resilience of the ericaceous ecosystem. Current knowledge of Erica –fire relationships is based on studies of modern vegetation, lacking a longer time perspective that can shed light on baseline conditions for the fire feedback. We hypothesize that fire has influenced Erica communities in the Bale Mountains at millennial time-scales. To test this, we (1) identify the fire history of the Bale Mountains through a pollen and charcoal record from Garba Guracha, a lake at 3950 m.a.s.l., and (2) describe the long-term bidirectional feedback between wildfire and Erica, which may control the ecosystem's resilience. Our results support fire occurrence in the area since ca 14 000 years ago, with particularly intense burning during the early Holocene, 10.8–6.0 cal ka BP. We show that a positive feedback between Erica abundance and fire occurrence was in operation throughout the Lateglacial and Holocene, and interpret the Ericaceous Belt of the Ethiopian mountains as a long-term fire resilient ecosystem. We propose that controlled burning should be an integral part of landscape management in the Bale Mountains National Park.