We have developed a method to capture the essential conformational dynamics of folded biopolymers using statistical analysis of coarse-grained segment-segment contacts. Previously, the residue-residue contact analysis of simulation trajectories was successfully applied to the detection of conformational switching motions in biomolecular complexes. However, the application to large protein systems (larger than 1000 amino acid residues) is challenging using the description of residue contacts. Also, the residue-based method cannot be used to compare proteins with different sequences. To expand the scope of the method, we have tested several coarse-graining schemes that group a collection of consecutive residues into a segment. The definition of these segments may be derived from structural and sequence information, while the interaction strength of the coarse-grained segment-segment contacts is a function of the residue-residue contacts. We then perform covariance calculations on these coarse-grained contact matrices. We monitored how well the principal components of the contact matrices is preserved using various rendering functions. The new method was demonstrated to assist the reduction of the degrees of freedom for describing the conformation space, and it potentially allows for the analysis of a system that is approximately tenfold larger compared with the corresponding residue contact-based method. This method can also render a family of similar proteins into the same conformational space, and thus can be used to compare the structures of proteins with different sequences.

The Barbary macaque Macaca sylvanus is imperiled throughout its distribution range in north-west Africa. In the summers of 2009 and 2013 we used the piecewise line-transect distance sampling method to study the southernmost population in the High Ourika valley, in the western High Atlas of Morocco. This rugged mountainous area is dominated by degraded fruit-poor environments, mostly holm oak Quercus rotundifolia forest patches. We located four and two groups in 2009 and 2013, respectively, and estimated population sizes of 122 and 84 individuals. The mean group size was 12 individuals in 2009 and 46 in 2013. The estimated mean density (individuals per km2) varied among groups (10–171), with a mean of 27. The population structure varied significantly among groups and years. Our records comprised 24.8 and 20% adult males, 24.8 and 22% adult females, 11 and 13% subadults, 13 and 17% juveniles and 26.4 and 26.3% infants in 2009 and 2013, respectively. In both years 50–56% of the population consisted of young individuals (subadults excluded). The mean sex ratio among adults was 1 : 1. The apparent fecundity rate was 1.06 infants per adult female. We propose conservation actions to protect this peripheral population of Barbary macaques.

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13–amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

The most ancient processes for energy production in the evolution of life involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13 amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe]-hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase (ACS), two ancient, extant proteins central to metabolism. These experimental results clearly demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.