Microsecond Scale Replica Exchange Molecular Dynamic Simulation of Villin Headpiece: An Insight into the Folding Landscape

Abstract

Reaching the experimental time scale of millisecond is a grand challenge for protein folding simulations. The development of advanced Molecular Dynamics techniques like Replica Exchange Molecular Dynamics (REMD) makes it possible to reach these experimental timescales. In this study, an attempt has been made to reach the multi microsecond simulation time scale by carrying out folding simulations on a three helix bundle protein, Villin, by combining REMD and Amber United Atom model. Twenty replicas having different temperatures ranging from 295 K to 390 K were simulated for 1.5 μs each. The lowest Root Mean Square Deviation (RMSD) structure of 2.5 Å was obtained with respect to native structure (PDB code 1VII), with all the helices formed. The folding population landscapes were built using segment-wise RMSD and Principal Components as reaction coordinates. These analyses suggest the two-stage folding for Villin. The combination of REMD and Amber United Atom model may be useful to understand the folding mechanism of various fast folding proteins     

New maimetshid wasps in Cretaceous amber from Myanmar (Insecta: Hymenoptera)

The extinct, exclusively Cretaceous wasp family Maimetshidae is newly recorded from Earliest Cenomanian Burmese amber. Two new genera and species are described. Burmaimetsha concava gen. et sp. nov., based on a male and a female, is most similar to Guyotemaimetsha Perrichot, Nel & Néraudeau, from Albian-Cenomanian French amber, but differs in its larger mandibles, distinctly concave face, elongate antennomeres, and forewing with cell [1Rs] smaller and fourth abscissa of Rs shorter. Maimetshasia kachinensis gen. et sp. nov., is based on a male, and is characterized by asymmetric mandibles with two and three teeth, by its forewing venation without cross-vein 2rs-m, with cell [1M] large and trapezoidal, and vein 2Rs + M very short, and by the hind wing without a free apex of Rs. The family was evidently widespread in the Cretaceous, and the new records extend the paleobiogeographical range to the South-East of Eurasia. A discussion about the possible biology of Maimetshidae is provided.     

The oldest known chironomids of the tribe Tanytarsini (Diptera: Chironomidae) indicate plesiomorphic character states

Taxonomic studies on chironomids of the tribe Tanytarsini recorded in Eocene Baltic amber from the Rovno region have revealed two new species: Archistempellina perkovskyi and Stempellinella ivanovae. Both species display interesting characters supporting evolutionary trends in the tribe. A. perkovskyi nov. sp. combines plesiomorphic characters, thus consolidating the hypothesis that the genus Archistempellina is one of the basal lineages of the tribe Tanytarsini. The antennal flagellum composed of 13 discernible segments found in S. ivanovae nov. sp. is defined as a plesiomorphic character state opposite to a reduced number of flagellomeres in extant species; the nipple-like process on the apex of the gonostylus is recognised as a unique character in the Tanytarsini and a possible homologue of the horn-like tip of the gonostylus known from several extant species of the genus Stempellinella Brundin. A key to determination of all genera and species of the Tanytarsini recorded in the Eocene is presented. Notes on evolutionary trends in the tribe are also provided.     

On the systematic position of Baltimartyria Skalski, 1995 and description of a new species from Baltic amber (Lepidoptera, Micropterigidae)

This paper describes a rare case of a male moth in Baltic amber in an excellent position for establishing a species. The moth represents the second species of the genus Baltimartyria Skalski, 1995, described herein as Baltimartyria rasnitsynisp. n. The detection of this new species prompts research on the systematic position of the genus within the family Micropterigidae. The genus was found to provide none of the apomorphic characters that would allow placement in one of the monophyletic lineages within the family. The genus is provisionally assigned to the "southern sabatincoid group", a weakly supported assemblage of Southern Hemisphere genera. The sister genus has still to be determined. Baltimartyria is the first North Hemisphere representative in this group. Some general aspects of historical biogeography relevant for the group are briefly discussed.     

A new scorpion fossil from the Cretaceous amber of Myanmar (Burma). New phylogenetic implications

A fossil scorpion belonging to a new family, genus and species, Chaerilobuthus complexus gen. n., sp. n., is described from Cretaceous amber of Myanmar (Burma). This is the third species and the fourth scorpion specimen to have been found and described from Burmese amber. The new family seems quite distinct from the family Archaeobuthidae Lourenço, 2001 described from Cretaceous amber of Lebanon.     

Ancient butterfly-ant symbiosis: direct evidence from Dominican amber

Although symbiotic association with ants is pervasive in the butterfly families Lycaenidae and Riodinidae the age of these symbioses has never been estimated explicitly. Here we report the first known fossil riodinid caterpillar. This fossil can be dated minimally between 15 and 20 Ma old, and confidently placed in the extant genus Theope. Differing little from modern day Theope, this fossil from Dominican amber provides direct evidence that secretory and acoustical organs used by modern caterpillars to mediate symbioses with ants have been highly developed at least since the Miocene. This fossil therefore becomes the point of reference for future studies using molecular clock methods for dating these symbioses within the riodinid butterflies. Modern evidence, and the abundance of dolichoderine ants in Dominican amber (now extinct in the West Indies) imply that specialized symbiotic relationships between Theope caterpillars and these ants were likely in existence at least 15 Ma ago. The current distribution of neotropical riodinid butterfly and ant faunas indicates the extinction in the West Indies of at least two unrelated taxa that formed a tightly linked symbiotic association, which persisted to the present elsewhere. <br>     

The Search for New Amber Ingredients

There is a constant need for developing new fragrance ingredients in the flavor and fragrance industry, as it allows perfumers to create unique and differentiating perfumes for fine as well as functional products. Among all the categories of notes used in perfume creation, amber notes are indispensible and ubiquitous in their presence in all perfumes. Not only amber notes impart high performance and substantivity to fragrances, but they are paramount in the development of classic and legendary fragrances. This article is based on the plenary lecture delivered at the flavor & fragrance 2013 conference of the German Chemical Society in Leipzig, Germany. The strategy, rationale, and the various synthetic approaches that led to the discovery of two new very powerful, woody, amber materials, Amber Xtreme^® ( 1 ) and Trisamber^® ( 2 ), are delineated.     

A new species of Chresmodidae from Mid-Cretaceous amber discovered in Myanmar

The extinct new species,Chresmoda chikuni Zhang & Ge,sp.nov.is described from the Mid-Cretaceous amber from northem Myanmar.This amber insect exhibits a very peculiar combination of derived characters like strongly elongated,free coxa,non-clawed pretarsus.The type specimens are deposited in the Three Gorges Entomological Museum,Chongqing,China.     

Bird's nest fungi (Nidulariales: Nidulariaceae) in Baltic and Dominican amber

Nidula baltica sp. nov. and Cyathus dominicanus sp. nov. are described from Cenozoic Baltic and Dominican amber. These are the first fossil members of the Family Nidulariaceae and show that the basic characteristics of this group were already established some 40–50 million years ago.