A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

2005 ◽  
Vol 60 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Qiaojun Fang ◽  
David Shortle
Keyword(s):  
Side Chain ◽  
Statistical Potentials ◽  
Local Side

scholarly journals Prion disease susceptibility is affected by  -structure folding propensity and local side-chain interactions in PrP

2010 ◽  
Vol 107 (46) ◽  
pp. 19808-19813 ◽  
Author(s):  
M. Q. Khan ◽  
B. Sweeting ◽  
V. K. Mulligan ◽  
P. E. Arslan ◽  
N. R. Cashman ◽  
...  
Keyword(s):  
Prion Disease ◽  
Disease Susceptibility ◽  
Side Chain ◽  
Local Side

scholarly journals An Algorithm for Computing Side Chain Conformational Variations of a Protein Tunnel/Channel

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2459
Author(s):  
Udeok Seo ◽  
Ku-Jin Kim ◽  
Beom Kang
Keyword(s):  
Amino Acids ◽  
Maximum Size ◽  
Protein Molecule ◽  
Divide And Conquer ◽  
Side Chain ◽  
Conformational Variations ◽  
Novel Method ◽  
Pass Through ◽  
Chain Conformations ◽  
Local Side

In this paper, a novel method to compute side chain conformational variations for a protein molecule tunnel (or channel) is proposed. From the conformational variations, we compute the flexibly deformed shapes of the initial tunnel, and present a way to compute the maximum size of the ligand that can pass through the deformed tunnel. By using the two types of graphs corresponding to amino acids and their side chain rotamers, the suggested algorithm classifies amino acids and rotamers which possibly have collisions. Based on the divide and conquer technique, local side chain conformations are computed first, and then a global conformation is generated by combining them. With the exception of certain cases, experimental results show that the algorithm finds up to 327,680 valid side chain conformations from 128~1233 conformation candidates within three seconds.

scholarly journals Multi-State Design of Flexible Proteins Predicts Sequences Optimal for Conformational Change

2019 ◽  
Author(s):  
Marion Sauer ◽  
Alexander M. Sevy ◽  
James E. Crowe ◽  
Jens Meiler
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Sequence Space ◽  
Sequence Conservation ◽  
Side Chain ◽  
Similarity Metrics ◽  
Local Similarity ◽  
Contact Map ◽  
Chain Conformations ◽  
Local Side

AbstractComputational protein design of an ensemble of conformations for one protein – i.e., multi-state design – determines the side chain identity by optimizing the energetic contributions of that side chain in each of the backbone conformations. Sampling the resulting large sequence-structure search space limits the number of conformations and the size of proteins in multi-state design algorithms. Here, we demonstrated that the REstrained CONvergence (RECON) algorithm can simultaneously evaluate the sequence of large proteins that undergo substantial conformational changes, such as viral surface glycoproteins. Simultaneous optimization of side chain conformations across all conformations resulted in an increase of 30% to 40% in sequence conservation when compared to single-state designs. More importantly, the sampled sequence space of RECON designs resembled the evolutionary sequence space of functional proteins. This finding was especially true for sequence positions that require substantial changes in their local environment across an ensemble of conformations. To quantify this rewiring of contacts at a certain position in sequence and structure, we introduced a new metric designated ‘contact proximity deviation’ that enumerates contact map changes. This measure allows mapping of global conformational changes into local side chain proximity adjustments, a property not captured by traditional global similarity metrics such as RMSD or local similarity metrics such as changes in φ and ψ angles.Author SummaryMulti-state design can be used to engineer proteins that need to exist in multiple conformations or that bind to multiple partner molecules. In essence, multi-state design selects a compromise of protein sequences that allow for an ensemble of protein conformations, or states, associated with a particular biological function. In this paper, we used the REstrained CONvergence (RECON) algorithm with Rosetta to show that multi-state design of flexible proteins predicts sequences optimal for conformational change, mimicking mutation preferences sampled in evolution. Modeling optimal local side chain physicochemical environments within an ensemble selected significantly more native-like sequences than selections performed when all conformations states are designed independently. This outcome was particularly true for amino acids whose local side chain environment change between conformations. To quantify such contact map changes, we introduced a novel metric to show that sequence conservation is dependent on protein flexibility, i.e., changes in local side chain environments between stated limit the space of tolerated mutations. Additionally, such positions in sequence and structure are more likely to be energetically frustrated, at least in some states. Importantly, we showed that multi-state design over an ensemble of conformations (space) can explore evolutionary tolerated sequence space (time), thus enabling RECON to not only design proteins that require multiple states for function but also predict mutations that might be tolerated in native proteins but have not yet been explored by evolution. The latter aspect can be important to anticipate escape mutations, for example in pathogens or oncoproteins.

Electroluminescent properties of side-chain naphthalimide-derivated polymers

1998 ◽  
Vol 95 (6) ◽  
pp. 1351-1354 ◽  
Author(s):  
C.-M. Bouché ◽  
P. Le Barny ◽  
H. Facoetti ◽  
F. Soyer ◽  
P. Robin
Keyword(s):  
Side Chain

Local Treatment of Recent Arterial Thromboembolic Occlusions with Brinase

1975 ◽  
Vol 34 (02) ◽  
pp. 498-503 ◽  
Author(s):  
D Nyman ◽  
M. A da Silva ◽  
L. K Widmer ◽  
F Duckert
Keyword(s):  
Side Effects ◽  
Local Treatment ◽  
Before And After ◽  
Local Side

SummaryBrinase was administered intra-arterially in 16 patients with thrombotic or embolic arterial occlusions. Angiography could be performed before and after treatment in 13 patients. Thrombolysis was obtained in 3 of 9 patients with thrombotic and in 3 of 4 patients with embolic occlusions. In 3 patients severe local side effects occurred.

Evidence for Impaired Hepatic Vitamin K1 Metabolism in Patients Treated with N-Methyl-Thiotetrazole Cephalosporins

1984 ◽  
Vol 51 (03) ◽  
pp. 358-361 ◽  
Author(s):  
H Bechtold ◽  
K Andrassy ◽  
E Jähnchen ◽  
J Koderisch ◽  
H Koderisch ◽  
...  
Keyword(s):  
Protein C ◽  
Oral Intake ◽  
Bleeding Complications ◽  
Side Chain ◽  
Acute Administration ◽  
Vitamin K1 ◽  
New Class ◽  
Parenteral Alimentation ◽  
Hepatocellular Regeneration ◽  
Echis Carinatus

SummaryIn 8 patients on no oral intake and with parenteral alimentation, administration of cephalosporins with N-methyl-thiotetrazole side chain (moxalactam, cefamandole), was associated with prolongation of prothrombin time, appearance in the circulation of descarboxy-prothrombin (counter immunoelectrophoresis and echis carinatus assay) and diminution of protein C. Acute administration of 10 mg vitamin Ki was followed by the transient appearance of vitamin K1 2,3-epoxide, indicating an impaired hepatocellular regeneration of vitamin K1 from the epoxide. Impaired hepatic vitamin K1 metabolism, tentatively ascribed to the N-methyl-thiotetrazole group, is one (but possibly not the only) cause of bleeding complications and depression of vitamin K1dependent procoagulants in patients treated with the new class of cephalosporins.

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