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1 rock and as inclusions in fossilized resins (amber).
2 n Collembola (the first is also preserved in amber).
3 otransistors from 495 nm (blue) to 590 nm (amber).
4 re studied with the QM/MM method ONIOM(B3LYP:AMBER).
5 iments using a 20-million-year-old Dominican amber.
6 Ma older than the earliest prior records in amber.
7 croscopic "conservation traps" comparable to amber.
8 supported by the molecular modeling package AMBER.
9 f any phytophagous insect group preserved in amber.
10 emidid damselfly from mid-Cretaceous Burmese amber.
11 force fields available for RNA, the parmbsc0 AMBER.
14 ling and molecular dynamics simulations with AMBER 6.0, investigating a T7 DNA polymerase primer-temp
17 e potentials, including a new variant of the AMBER-99 force field, denoted AMBER-99 phi, which shows
19 variant of the AMBER-99 force field, denoted AMBER-99 phi, which shows improved agreement with experi
20 Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA(Pyl) mutants were
23 ing evidence for melanin pigmentation in the amber and compression fossils, but Raman spectral bands
24 ized orthogonal translation system that uses amber and evolved quadruplet-decoding transfer RNAs to e
27 poson as demonstrated by the substitution of amber and/or in-frame deletions in six different genes.
30 mbion compactus gen. et sp. nov., in Burmese amber ( approximately 99 million years old), displaying
32 (new family)] from Early Cretaceous Burmese amber (approximately 100 million years before the presen
33 eptor (A), and a photo-insensitive molecule (Amber) as a nonfluorescent (N) place holder: namely, NDA
34 ular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squ
38 art and a stop that can even be a suppressed amber codon 22 nucleotides further downstream from the r
39 yl- l-phenylalanine (Bpa) in response to the amber codon allowed the biosynthesis of Bpa-substituted
40 ded this unique amino acid in response to an amber codon allowing a single 1 to be placed at any loca
41 n from approximately 20% to >60% on a single amber codon and from <1% to >20% on two amber codons.
43 stal structure of MtmB demonstrated that the amber codon codes for pyrrolysine, the 22nd genetically
46 Pyrrolysine is an amino acid encoded by the amber codon in genes required for methylamine utilizatio
52 the radical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and in
55 ite-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalia
56 vo incorporation of unnatural amino acids by amber codon suppression is limited by release factor-1-m
57 S can be redesigned to achieve high-fidelity amber codon suppression through delivery of p-bromopheny
59 site-specific introduction into proteins via amber codon suppression using the wild-type pyrrolysyl-t
64 g the efficiency of suppression at a gene II amber codon upstream from the gene X start, the already
67 cognate orthogonal tRNA that recognizes the amber codon, are encoded on the plasmid pSUPAR6-L3-3SY,
68 ecodes a series of quadruplet codons and the amber codon, providing several blank codons on an orthog
69 efficiently incorporated at a predefined UAG amber codon, thereby competing with RF1 rather than RF2.
70 system that site-specifically--using the UAG amber codon--inserts Sec depending on the elongation fac
83 rrolysine requires the pylT gene product, an amber-decoding tRNA(Pyl) that is aminoacylated with pyrr
85 may have contributed to the formation of the amber droplets, but we find that the abundance of amber
86 droplets, but we find that the abundance of amber during the Carnian (ca. 230 Ma) is globally anomal
88 m mass spectrometry revealed the mass of the amber-encoded residue in MtmB, MtbB, and MttB as 237.2 +
90 and feather development of DIP-V-15103, the amber-entombed tail section that we recently reported [2
93 h a force field, the relative weights of the Amber ff03 all-atom potential supplemented by an explici
94 ll-atom molecular dynamics simulations using AMBER FF03 and the generalized-Born solvation model.
95 d-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation
97 "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structure
98 he relative weights of the components of the Amber ff03 potential on a large set of decoy structures
99 figurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A
101 h an optimized all-atom protein force field (Amber ff03w) and an accurate water model (TIP4P/2005) to
102 an 0.8 mus MD simulation computed using the Amber ff10 force field as well as to determine an atomic
105 s by using new generation TIP4P-Ew water and Amber ff99SB protein force fields, in which the NMR vali
107 g of residue charges for charged residues in Amber ff99SB( *) significantly improves their helix prop
112 hlights the unique preservation potential of amber for understanding the morphology and evolution of
114 inst various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years
115 h B3LYP/6-311+G(d,p) for the QM part and the AMBER force field for the MM part were used to examine t
116 Molecular dynamics (MD) simulations using AMBER force field in explicit solvent were run for over
117 g mini-protein designated as tc5b with a new AMBER force field parameter set developed based on conde
123 ble, those obtained using last generation of AMBER force-fields (BSC1 and BSC0OL15) show predictive p
129 ved in mid-Cretaceous ( approximately 99 Ma) amber from Kachin State, Myanmar [17], with plumage stru
131 preserved in Early Cretaceous (ca. 100 mya) amber from Myanmar, one described as Krishnatermes yoddh
133 f a green lacewing larva in Early Cretaceous amber from Spain with specialized cuticular processes fo
136 ring of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF
137 files can be used for CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/Open
139 itive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulat
142 ce by molecular mechanics calculations using AMBER has provided three-dimensional potential energy ma
143 sible traces of colour, while discoveries in amber have been disassociated from their source animals.
144 With the taxa reported herein, the Mexican amber holds the greatest diversity of fossil copepods wo
145 All the honeys, except for a Malaysian "Amber honey" stimulated the release of TNF-alpha from mo
148 roplebeia dominicana, recovered from Miocene amber in the Dominican Republic, that is 15-20 million y
149 esy in 16 million-year-old Miocene Dominican amber involving a springtail being transported by a mayf
152 anine-related phenotypic suppression of lacZ amber is enhanced by mutations in genes related to the p
154 rther recovery of arthropods in Carnian-aged amber is promising and will have profound implications f
155 The preservation of aquatic arthropods in amber is unusual but offers a unique insight into ancien
157 electronic-embedding approach (B3LYP/6-31G*:AMBER) level of theory and the S0-->S1 electronic-excita
158 ding approach (TD-B3LYP/6-31G*//B3LYP/6-31G*:AMBER) level of theory, are in very good agreement with
159 ies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenz
163 of carotenoids in six feathers preserved in amber (Miocene to mid-Cretaceous) and in a feather prese
167 with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielde
173 h a mutant N4 isolate (N4am229) harboring an amber mutation in Orf65 yielded virions containing (N4gp
175 o position 14 in firefly luciferase using an amber mutation or introducing the four-codon nucleotide
177 ther understand the role of gp32, we created amber mutations at codons 24 and 204 of gene 32, which e
178 he six mutants that we examined retained two amber mutations in gene 38 and had a different coiled-co
180 ne, was genetically encoded in E. coli by an amber nonsense codon and corresponding orthogonal tRNA/a
181 oded in Saccharomyces cerevisiae by using an amber nonsense codon and corresponding orthogonal tRNA/a
188 amino acids in response to three independent amber nonsense codons in sperm whale myoglobin or green
190 a complete set of orthogonal 21st synthetase-amber, ochre and opal suppressor tRNA pairs including th
193 roteins and for the regulated suppression of amber, ochre and opal termination codons in mammalian ce
194 using the beta-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the seri
195 lized pollination mode from Early Cretaceous amber of Spain, wherein four female thrips representing
198 gnificant criteria required for an efficient amber orthogonal suppressor tRNA are a CU(X)XXXAA antico
200 zations, parm99chi_YIL and parm99TOR, of the AMBER parm99 force field improve the agreement between s
201 arger rmsd value of 1.28 pH units, while the AMBER parm99 parameter set resulted in a considerably po
202 bly robust predictions, while that of PARSE, AMBER parm99, and AMBER ff03 performed more poorly.
203 cations according to packaging material (PET amber, PET transparent and tinplate can) and light expos
204 ambda, a negative model proposes that in the amber phages, unassembled capsid components are inhibito
205 om simulations under several variants of the AMBER potential in explicit solvent using a global distr
209 rich deposits of 99 million-year-old Burmese amber resolves ambiguity regarding sociality and diversi
211 t evidence in 99 million-year-old Cretaceous amber showing that hard ticks and ticks of the extinct n
212 tic affinities to those from coeval European ambers, showing a biotic interchange between the eastern
213 persists for at least 1 mus, whereas in the AMBER simulation, it remains highly dynamic; additional
214 The simulations were carried out using the Amber software on inexpensive GPUs, providing approximat
215 A. margulisae from Late Albian Penacerrada I amber (Spain) possess four pairs of rudimentary oostegit
216 McKellar et al. analyzed Late Cretaceous amber specimens from Canada and identified some filament
219 amino acid incorporation in response to the amber stop codon (UAG) in mammalian cells is commonly co
220 e a suppression-mimicking allele lacking the amber stop codon and extended 7 amino acids did not.
221 n of different amino acids in response to an amber stop codon by utilizing switchable designer transf
231 en reading frames (ORFs) that terminate with amber stop codons in the Escherichia coli genome, includ
232 nical translation machinery and can suppress amber stop codons to incorporate selenocysteine with hig
237 in vitro translation of mRNAs containing an amber-stop codon in the signal peptide in the presence o
238 The calculations were performed using the AMBER suite of programs and the parm94 force field, vali
239 ll-defined state-of-the-art MD protocol, the AMBER suite of programs, and the parm94 force field.
240 rried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field.
241 ) calculations were then performed using the AMBER suite to validate the newly generated force field.
247 growth rates and is mutually orthogonal with amber suppression, permitting the simultaneous incorpora
250 or U50:A64 base pairs increases the in vivo amber suppressor activity of initiator tRNA mutants that
252 mino acids (ncAAs) by introducing orthogonal amber suppressor aminoacyl-tRNA synthetase/tRNA pairs in
253 ylation modulates RAD52 function, we used an amber suppressor technology to substitute tyrosine 104 w
255 eRS (T415G) and a mutant yeast phenylalanine amber suppressor tRNA (ytRNAPheCUA_UG) into an E. coli e
256 ystem, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus
258 ichia coli that uses a plasmid to produce an amber suppressor tRNA regulated by the arabinose promote
260 suppressor tRNAs are less efficient than the amber suppressor tRNA THG73 (Tetrahymena thermophila G73
261 g aminoacyl-tRNA synthetases aminoacylate an amber suppressor tRNA with a desired unnatural amino aci
262 enes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on
263 on levels of the orthogonal Escherichia coli amber suppressor tRNA(CUA) and cognate aminoacyl-tRNA sy
268 don with high efficiency using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase (aaRS) p
270 was responsible for misacylating the initial amber suppressor version of the yeast tryptophanyl tRNA.
273 id residues in Ste2p with Bpa by engineering amber TAG stop codons into STE2 encoded on a plasmid.
274 ynthetase pair in Escherichia coli to decode amber (TAG), opal (TGA), and four-base (AGGA) codons.
275 rolysine, the 22nd amino acid, is encoded by amber (TAG=UAG) codons in certain methanogenic archaea a
276 a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a
277 gment of a fertile leaf preserved in Burmese amber that represents the first fossil evidence of the f
278 leaves enclosed in a piece of Eocene Baltic amber that share relevant morphological features with ex
280 (Staphylinidae) from mid-Cretaceous Burmese amber, the latter belonging to Oxyporinae, modern member
281 band (NEB) technique has been implemented in AMBER to calculate low-energy paths for conformational c
283 mino acid, because it is encoded by a single amber (UAG) codon in methylamine methyltransferase trans
284 The DNA template contains a complementary amber (UAG) codon instead of the normal initiation (AUG)
290 epatitis delta virus (HDV) antigenome at the amber/W site by the host RNA adenosine deaminase ADAR1 i
291 created and the effects of these changes on amber/W site editing, RNA replication, and virus product
292 econdary structure around the HDV genotype I amber/W site has been selected not for the highest editi
295 In addition, the structure adjacent to the amber/W site is suboptimal for editing, and this creates
296 cted secondary structure downstream from the amber/W site, a replication-competent HDV mutant that ex
299 rap-jaw ant from 99 million-year-old Burmese amber with head structures that presumably functioned as
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