QAUST:Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.

Simulation,construction and characterization of a multi-functional thrombolytic agent with anti-thrombosis activity

Prourokinase(scu-PA),a thrombolytic agent,was inserted between Gly118 and Ile119 with foreign anti-thrombosis functional motif(Lys-Gly-Asp-Trp-motif)to construct a multi-functional chimeric molecule.The molecular model of a chimera was simulated and pre-dicted.The recombinant chimeric protein was expressed by the baculovirus-insect cell expression system and puri-fied by affinity chromatography.The physico-chemical characteristics of the chimeric molecule were assayed.The thrombolytic activity was determined to be 90000 IU/mg of fibrinolytic special activity by the fibrin-plate method.The anti-thrombosis activities were also assayed with IC50 of 9.6 μM by an inhibition test of ADP-induced platelet aggregation.

The centrosymmetric to non-centrosymmetric transformation induced by alkaline-earth cations producing infrared nonlinear optical AeMn_(6)Ga_(6)S_(16)(Ae=Ca,Sr)

Non-centrosymmetric(NCS)structure is an indispensable prerequisite for second-order nonlinear optical(NLO)material.Currently,the mainstream approach for designing new NCS structures still relies on chemical substitution,necessitating an urgent infusion of fresh ideas.In this work,two isomorphic sulfides AeMn_(6)Ga_(6)S_(16)(Ae=Ca,1;Sr,2)are afforded by modifying the skeleton of centrosymmetric(CS)Mn_(2)Ga_(2)S_(5) via introducing strong electropositive alkaline-earth cations.Concretely,the incorporation of Ca^(2+)/Sr^(2+)cations allows the elementary[MnGaS_(9)]_(∞)chains to reconfigure into bumpy[MnS_(6)]-[GaS_(4)]layers in a new engagement manner,thus enabling the conversion from CS to NCS structure.Such modifications cause not only strong second-harmonic generation(SHG)responses(~1.5×benchmark AgGaS_(2)@1,700 nm),but also significantly feasible bandgaps(2.60-2.64 e V)compared to the sulfide Mn_(2)Ga_(2)S_(5)(1.36 e V),which ultimately facilitate ultrahigh laser-induced damage thresholds(4.4-6.6×AgGaS_(2)@1,064 nm for compounds 1 and 2).The present study offers an ingenious approach for the transformation of CS to NCS structure.

Two-dimensional Organic Metal Chalcogenides

Inorganic two-dimensional(2 D)materials have attracted tremendous interests recently.Controlled functionalization of 2 D materials can achieve additional functions and properties,but usually suffers from less modification ratio,poor controllability,defects and so on.2 D organic metal chalcogenide(OMC)materials with periodically arranged organic functional group between the inorganic analogues layers offer opportunities to develop adjustable electrical properties and extended applications.In this mini-review,we will provide an overview of the composition and preparation,band gap engineering,and conductivity modulation of the serial OMC materials and illustrate the application investigation such as biomimetic catalysis,photodetecting and chemiresistive gas sensing.

Atom Response Theory of Nonlinear Optical Responses and Its Applications

Second-order nonlinear optical(NLO)crystalline materials are fundamentally and technologically important for their ability to double or triple the frequency of lasers.This article provides a brief review of the atom response theory(ART)of NLO responses recently developed on the basis of the partial response functional method.The ART analysis enables one to quantitatively evaluate the contributions of individual constituent atoms to the second harmonic generation(SHG)response of a NLO crystal material on the basis of first principles DFT calculations.The general partitioning principles developed in our recent work provide the conceptual foundation for determining the functional motifs of SHG responses.In this mini review we will focus on the concepts and principles as well as on applications with examples.Some practically important empirical rules resulting from the ART studies will also be reviewed.