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Diffusion-based determination of protein homodimerization on reconstituted membrane surfaces
( Tyler A. Jepson ),( Jean K. Chung ) 생화학분자생물학회 2021 BMB Reports Vol.54 No.3
The transient interactions between cellular components, particularly on membrane surfaces, are critical in the proper function of many biochemical reactions. For example, many signaling pathways involve dimerization, oligomerization, or other types of clustering of signaling proteins as a key step in the signaling cascade. However, it is often experimentally challenging to directly observe and characterize the molecular mechanisms such interactions―the greatest difficulty lies in the fact that living cells have an unknown number of background processes that may or may not participate in the molecular process of interest, and as a consequence, it is usually impossible to definitively correlate an observation to a well-defined cellular mechanism. One of the experimental methods that can quantitatively capture these interactions is through membrane reconstitution, whereby a lipid bilayer is fabricated to mimic the membrane environment, and the biological components of interest are systematically introduced, without unknown background processes. This configuration allows the extensive use of fluorescence techniques, particularly fluorescence fluctuation spectroscopy and single-molecule fluorescence microscopy. In this review, we describe how the equilibrium diffusion of two proteins, K-Ras4B and the PH domain of Bruton’s tyrosine kinase (Btk), on fluid lipid membranes can be used to determine the kinetics of homodimerization reactions. [BMB Reports 2021; 54(3): 157-163]
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정상훈(S.H. Chung),권위남(W.N. Kwon),권보섭(B.S. Kwon),진성기(S.K. Jean),윤현수(H. Yoon),조정완(J.W. Cho) 한국정보과학회 2000 한국정보과학회 학술발표논문집 Vol.27 No.2Ⅲ
현재 인터넷은 매우 빠른 속도로 커가고 있으며 기존의 인터넷 하부구조(infrastructure), 특히 라우터에 커다란 부담이 되고 있다. IP 주소 검색은 라우터에 들어오는 패킷의 출력 링크를 찾기 위해 전송 테이블에서 가장 길게 일치하는 프리픽스를 찾는 것이다. 이러한 작업은 매우 복잡하고 고속의 라우터에 커다란 병목이 되고 있으며 이를 해소하기 위해서는 하드웨어기반의 빠른 IP 주소 검색 기법이 필요하다. 본 논문은 유니 캐스트 상에서 전송 테이블의 크기와 검색 시간을 줄이고 점차적인 갱신이 가능한 하드웨어기반의 알고리즘을 제시하고 다른 하드웨어 기반의 알고리즘과 성능을 비교한다. 제시한 알고리즘은 작은 크기의 SRAM과 단순한 로직의 하드웨어로 구현되기 때문에 값이 싸고 파이프라인으로의 구성이 가능하기 때문에 빠른 IP 주소 검색이 가능하다. 10ns의 SRAM으로 구현할 경우, 초당 100×10^6의 검색이 가능하고 이는 지금까지 제안된 알고리즘보다 빠른 검색을 제공할 수 있다.
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Thielges, Megan C.,Axup, Jun Y.,Wong, Daryl,Lee, Hyun Soo,Chung, Jean K.,Schultz, Peter G.,Fayer, Michael D. American Chemical Society 2011 The journal of physical chemistry. B, Condensed ma Vol.115 No.38
<P>Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jpcbfk/2011/jpcbfk.2011.115.issue-38/jp206986v/production/images/medium/jp-2011-06986v_0004.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/jp206986v'>ACS Electronic Supporting Info</A></P>
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