중간단계의 구조적 안정성을 통한 HubWA 단백질의 접힘 (folding) 반응 탐색

박순호 대한화학회 2023 대한화학회지 Vol.67 No.2

The contribution of hydrophobic residues to the protein folding reaction was studied by using HubWA variant proteins with I and L to V mutation. Folding kinetics of all V variant proteins was observed to be satisfied by a three-state on- pathway mechanism, U ⇌ I ⇌ N, where U, I, and N represent unfolded, intermediate, and native state, respectively. Three- state folding reaction was quantitatively analyzed and the free energy of folding of each elementary reactions and overall fold- ing reaction, ΔGoUI, ΔGoIN, and ΔGoUN, were obtained. From the ratio of free energy difference between the variant protein and HubWA, ΔΔGoUI/ΔΔGoUN (ΔΔGoUI = ΔGoUI (variant protein) − ΔGoUI (HubWA) and ΔΔGoUN = ΔGoUN (variant protein) − ΔGoUN (HubWA)), the contribution of hydrophobic residues to HubWA folding was analyzed. The residues which are located in the hydrophobic core between α-helix and β-sheet, I3, I13, L15, I30, L43, I61 and L67, showed ΔΔGoUI/ΔΔGoUN value of ~0.5 when each of these residues was mutated to V, indicating that these residues form relatively solid hydrophobic core in the intermediate state. Residues located at the end of secondary structures and loop, I23, L69 and I36 showed ΔΔGoUI/ΔΔGoUN value below 0.4 when each of these residues was mutated to V, indicating that the region containing these residues are loosely formed in the intermediate state. V17A, L50V and L56V showed fairly high ΔΔGoUI/ΔΔGoUN value of ~0.8. Since L50 and L56 are located in the region containing long loop (residue 46 to 62), it is suggested that the high ΔΔGoUI/ΔΔGoUN value of these residues prevents the formation of aggregate at the early stage of folding reaction. HubWA 단백질을 모델로 삼아 소수성 아미노산이 folding 반응에 끼치는 영향을 탐색하기 위하여 HubWA에 있는 I와 L 을 V로 치환한 변이 단백질의 folding kinetics를 측정하였다 . 변이 단백질의 folding kinetics는 HubWA 단백질과 마찬가지로 three- state on-pathway mechanism(U ⇌ I ⇌ N, U는 unfolded 상태 , I는 중간단계 , N은 native 상태를 의미한다 )을 따르는 것으로 나타났다. Folding kinetics 분석을 통하여 three-state 반응의 elementary 반응과 전체 반응의 자유에너지인 ΔGoUI, ΔGoIN, ΔGoUN을 얻었고 , 변이 단백질의 자유에너지와 HubWA 단백질의 자유에너지의 차(ΔΔGoUI = ΔGoUI(변이 단백질 )–ΔGoUI(HubWA), ΔΔGoUN = ΔGoUN (변이 단백질 ) – ΔGoUN(HubWA))의 비인 ΔΔGoUI/ΔΔGoUN를 통하여 중간단계가 전체 folding 반응에 끼치는 영향을 각 소수성 잔기 별로 알아볼 수 있었다 . HubWA의 입체구조에서 α-helix와 β-sheet가 상호작용하는 소수성 코어에 위치하는 아미노산인 I3, I13, L15, I30, L43, I61, L67을 V로 치환한 변이 단백질의 ΔΔGoUI/ΔΔGoUN 값이 ~0.5로 나타난 점은 이들 아미노산이 중간단계에서native 상태보다는 느슨하지만 비교적 견고한 구조를 이루는 것으로 해석되었다 . HubWA 입체구조에서 α-helix의 아미노말단에위치하는 I23, 특정 이차구조가 없는 부위에 위치하는 I36, β-strand 5의 카복실말단에 위치하는 L69를 V로 치환한 변이 단백질의 ΔΔGoUI/ΔΔGoUN 값이 0.4 이하로 나타난 것은 이들 아미노산 잔기가 중간단계에서는 비교적 느슨한 구조를 이루다 중간단계에서 native 단계로 진행하는 folding 과정의 후반부에 HubWA의 입체구조에 견고하게 편입되는 것으로 해석되었다 . HubWA의입체구조에서 두 번째 β-strand의 카복실말단에 위치한 V17, 짧은 네 번째 β-strand의 카복실말단에 위치한 L50, 짧은 310-helix의아미노말단에 위치한 L56이 중간단계에서 서로 상호작용을 하는 점은 이들 아미노산을 V로 치환한 변이 단백질의 ΔΔGoUI/ΔΔGoUN 값이 0.8 이상으로 나타난 점을 통하여 알 수 있었다 . L50과 L56은 짧은 β-strand와 310-helix를 제외하고 특별한 이차구조가 존재하지 않는 부위 (46번째 아미노산 잔기부터 62번째 아미노산 잔기 까지 )에 위치하는데 , 이들 아미노산이 V17과 더불어 folding 반응의 초기에 견고하게 상호작용을 하는 것은 HubWA단백질이 folding 과정의 초기에 응집체를 형성하는 것을 막아주는 역할을하는 것으로 생각되었다.

1.8V 12-bit 10MSPS Folding/Interpolation CMOS Analog-to-Digital Converter의 설계

손찬(Chan Son),김병일(Byung-Il Kim),황상훈(Sang-Hoon Hwang),송민규(Min-Kyu Song) 대한전자공학회 2008 電子工學會論文誌-SD (Semiconductor and devices) Vol.45 No.11

본 논문에서는 1.8V 12-bit 10MSPS CMOS A/D 변환기 (ADC) 를 제안한다. 제안하는 ADC 는 12-bit 의 고해상도를 구현하기 위해 even folding 기법을 이용한 folding/interpolation 구조로 설계하였다. ADC 의 전체 구조는 2단으로 구성된 folding/interpolation 구조로써, 각각의 folding rate (FR) 은 8을 적용하였고, interpolation rate (IR) 은 1<SUP>st</SUP> stage 에서 8, 2<SUP>nd</SUP> stage 에서 16을 적용하여 설계함으로써 고해상도를 만족시키기 위한 최적의 구조를 제안하였다. 또한 SNR 을 향상시키기 위하여 folding/interpolation 구조 자체를 cascaded 형태로 설계하였으며, distributed track and hold 를 사용하였다. 제안하는 ADC 는 0.18㎛ 1-poly 4-metal n-well CMOS 공정을 사용하여 제작되었다. 시제품 ADC 는 측정결과 10MSPS 의 변환속도에서 약 46㏈의 SNDR 성능특성을 보이며, 유효 칩 면적은 2000㎛×1100㎛ 의 면적을 갖는다. In this paper, an 1.8V 12-bit 10MSPS CMOS A/D converter (ADC) is described. The architecture of the proposed ADC is based on a folding and interpolation using an even folding technique. For the purpose of improving SNR, cascaded-folding cascaded-interpolation technique, distributed track and hold are adapted. Further, a digital encoder algorithm is proposed for efficient digital process. The chip has been fabricated with 0.18㎛ 1-poly 4-metal n-well CMOS technology. The effective chip area is 2000㎛×1100㎛ and it consumes about 250㎽ at 1.8V power supply. The measured SNDR is about 46㏈ at 10㎒ sampling frequency.

Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium

Chakrabarti, Shaon,Hyeon, Changbong,Ye, Xiang,Lorimer, George H.,Thirumalai, D. National Academy of Sciences 2017 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.114 No.51

<P><B>Significance</B></P><P>Molecular chaperones have evolved to assist the folding of proteins and RNA, thus avoiding the deleterious consequences of misfolding. Thus, it is expected that increasing chaperone concentrations should enhance the yield of native states. While this has been observed in GroEL-mediated protein folding, experiments on <I>Tetrahymena</I> ribozyme folding assisted by CYT-19 surprisingly show the opposite trend. Here, we reconcile these divergent experimental observations by developing a unified theory of chaperone-assisted protein and RNA folding. We show that these ATP-fueled machines drive their substrates out of equilibrium, maximizing the nonequilibrium native yield in a given time rather than the absolute yield or folding rate. The theory predicts that in vivo the number of chaperones is regulated to optimize their functions.</P><P>Molecular chaperones facilitate the folding of proteins and RNA in vivo. Under physiological conditions, the in vitro folding of <I>Tetrahymena</I> ribozyme by the RNA chaperone CYT-19 behaves paradoxically; increasing the chaperone concentration reduces the yield of native ribozymes. In contrast, the protein chaperone GroEL works as expected; the yield of the native substrate increases with chaperone concentration. The discrepant chaperone-assisted ribozyme folding thus contradicts the expectation that it operates as an efficient annealing machine. To resolve this paradox, we propose a minimal stochastic model based on the Iterative Annealing Mechanism (IAM) that offers a unified description of chaperone-mediated folding of both proteins and RNA. Our theory provides a general relation that quantitatively predicts how the yield of native states depends on chaperone concentration. Although the absolute yield of native states decreases in the <I>Tetrahymena</I> ribozyme, the product of the folding rate and the steady-state native yield increases in both cases. By using energy from ATP hydrolysis, both CYT-19 and GroEL drive their substrate concentrations far out of equilibrium, thus maximizing the native yield in a short time. This also holds when the substrate concentration exceeds that of GroEL. Our findings satisfy the expectation that proteins and RNA be folded by chaperones on biologically relevant time scales, even if the final yield is lower than what equilibrium thermodynamics would dictate. The theory predicts that the quantity of chaperones in vivo has evolved to optimize native state production of the folded states of RNA and proteins in a given time.</P>

소피아 비조비티의 폴딩 기법을 활용한 제로 웨이스트 패션 디자인

도간오큠,서미희,이연희 복식문화학회 2022 服飾文化硏究 Vol.30 No.4

The purpose of this study is to understand the concept of zero-waste design and to apply Sophia Vyzoviti’s folding techniques to develop a zero-waste fashion design method that contributes to sustainable fashion design. In this study, we explore the method and characteristics of zero-waste fashion design based on the concept of folding described in Sophia Vyzoviti’s book on folding techniques. Using the autonomy of Sophia Vyzoviti’s folding technique, four changeable folding fashion designs were developed and produced, demonstrating zero-waste fashion design. The results were as follows. First, the development of fashion designs using Sophia Vyzoviti’s folding techniques enabled the development and production of free and creative zero-waste fashion designs that were three-dimensional, continuous, fluid, and full of potential. Second, the production of zero-waste patterns was further developed into a transformable fashion design that can be used with geometric patterns. These folding techniques produced a fashion design method that could transform one piece of clothing, demonstration the potential for maintenance of creativity using a zero-waste design based on these folding techniques. Third, the double-faced fabric, Neoprene, was chosen as an appropriate material as it emphasizes the depth of folding with application of two colors and its cotton/polyester blend that is suitable for folding.

Macromolecule-Assisted <i>de novo</i> Protein Folding

Choi, Seong Il,Son, Ahyun,Lim, Keo-Heun,Jeong, Hotcherl,Seong, Baik L. Molecular Diversity Preservation International (MD 2012 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.13 No.8

<P>In the processes of protein synthesis and folding, newly synthesized polypeptides are tightly connected to the macromolecules, such as ribosomes, lipid bilayers, or cotranslationally folded domains in multidomain proteins, representing a hallmark of <I>de novo</I> protein folding environments <I>in vivo</I>. Such linkage effects on the aggregation of endogenous polypeptides have been largely neglected, although all these macromolecules have been known to effectively and robustly solubilize their linked heterologous proteins in fusion or display technology. Thus, their roles in the aggregation of linked endogenous polypeptides need to be elucidated and incorporated into the mechanisms of <I>de novo</I> protein folding <I>in vivo</I>. In the classic hydrophobic interaction-based stabilizing mechanism underlying the molecular chaperone-assisted protein folding, it has been assumed that the macromolecules connected through a simple linkage without hydrophobic interactions and conformational changes would make no effect on the aggregation of their linked polypeptide chains. However, an increasing line of evidence indicates that the intrinsic properties of soluble macromolecules, especially their surface charges and excluded volume, could be important and universal factors for stabilizing their linked polypeptides against aggregation. Taken together, these macromolecules could act as folding helpers by keeping their linked nascent chains in a folding-competent state. The folding assistance provided by these macromolecules in the linkage context would give new insights into <I>de novo</I> protein folding inside the cell.</P>

1.2V 10b 500MS/s 단일채널 폴딩 CMOS A/D 변환기

문준호(Junho Moon),박성현(Sunghyun Park),송민규(Minkyu Song) 大韓電子工學會 2011 電子工學會論文誌-SD (Semiconductor and devices) Vol.48 No.1

본 논문에서는 LTE-Advanced, software defined radio(SRD)등 4G 이동통신 핵심기술에 응용 가능한 10b 500MS/s 0.13㎛ CMOS A/D 변환기(ADC)를 제안한다. 제안하는 ADC는 저전력 특성을 만족하기 위해 특별한 보정기법을 포함하지 않는 단일 채널 형태로 설계되었으며, 500MS/s의 고속 변환속도를 만족하기 위해 폴딩 신호처리 기법을 사용하였다. 또한 하위 7b ADC의 높은 folding rate(FR)을 극복하기 위해 cascaded 형태의 폴딩-인터폴레이팅 기법을 적용하였으며, 폴딩 버스에서 발생하는 기생 커패시턴스에 의한 주파수 제한 및 전압이득 감소를 최소화하기 위해 folded cascode 출력단을 갖는 폴딩 증폭기를 설계하였다. 제안하는 ADC는 0.13㎛ 1P6M CMOS 공정으로 설계되었으며 유효면적은 1.5㎟이다. 시제품 ADC의 INL, DNL은 10b 해상도에서 각각 2.95LSB, 1.24LSB 수준으로 측정되었으며, 입력주파수 9.27MHz, 500MHz의 변환속도에서 SNDR은 54.8dB, SFDR은 63.4dBc의 특성을 보인다. 1.2V(1.5V)의 전원전압에서 주변회로를 포함한 전체 ADC의 전력소모는 150mW(300μW/MS/s)이다. A 10b 500MS/s 0.13㎛ CMOS ADC is proposed for 4G wireless communication systems such as a LTE-Advanced and SDR. The ADC employs a calibration-free single-channel folding architecture for low power consumption and high speed conversion rate. In order to overcome the disadvantage of high folding rate, at the fine 7b ADC, a cascaded folding-interpolating technique is proposed. Further, a folding amplifier with the folded cascode output stage is also discussed in the block of folding bus, to improve the bandwidth limitation and voltage gain by parasitic capacitances. The chip has been fabricated with 0.13㎛ 1P6M CMOS technology, the effective chip area is 1.5㎟. The measured results of INL and DNL are within 2.95LSB and 1.24LSB at 10b resolution, respectively. The SNDR is 54.8dB and SFDR is 63.4dBc when the input frequency is 9.27MHz at sampling frequency of 500MHz. The ADC consumes 150mW(300μW/MS/s) including peripheral circuits at 500MS/s and 1.2V(1.5V) power supply.

디지털 건축디자인으로서 '주름(Fold)'에 관한 연구 : 질 들뢰즈의 '주름(Fold)'사유와 피터 아이젠만의 '접기(Folding)'기법을 중심으로 through G. Deleuze's 'fold' thought and Peter Eisenman's 'folding'

강훈,이동언 대한건축학회 2004 대한건축학회논문집 Vol.20 No.11

The keyword to solve Deleuze's folding thought is the virtual. It contains all relations changing endlessly by differences as it is refusing the transcendental and absolute center but maintaining consistency. It makes it possible for the new approaching methods to escape from the previous established ones. It opens the way expressing the immanent life and the variety as endless differences. The architecture that always intensifies the virtual can be unfolded if the folding thought can be architecturally actualized. So, this paper interpret with the digital form making languages and the digital form transforming methods as diagrams which Peter Eisenman used it in his works on the basis of the Deleuze's folding thought. Furthermore, it propose the new digital form creating methods that can express fold's thought and that are excluded in Eisenman's methods. The suggested digital form creating methods can be thought as the most proper ones of making an architectural form closer to Deleuze's folding thought. These methods showed possibilities that they transform the digital design concepts combined with the contemporary architectural theory based on Deleuze into architecture.

Development of men’s jacket design applying nature’s folding characteristics

Hee Jung Kim,Youn Mee Lee,Younhee Lee 복식문화학회 2020 服飾文化硏究 Vol.28 No.6

This study aims to derive the criteria of folding techniques and their characteristics through analysis of literature and previous studies. This will be realized by performing a case study on male fashion design and folding. It will propose diverse directions and data for male fashion design, by making men’s jackets using a folding technique. The concept and terms of folding were clarified through examination of existing literature and previous studies. Specifically, four pieces were created with motifs of the four seasons. Among the types of pleats expressed in the works, composition pleats include double ruffles, gathers, and draperies, while processed ones include box pleats, knife pleats, and accordion pleats. This study expresses continuity, fluidity, scalability, and ambiguity through the use of such pleats. The results of the production are as follows. First, in terms of the continuous use of regular and repetitive pleats, a possibility of rich pleats was confirmed because they varied depending on the gap between the pleat and target material. Second, in liquid but irregular pleats, diverse moods were created by the pleat movement. The overlapping of repeated pleats expresses diverse spaces and shapes in a 3D extended silhouette. Third, in pleat classification, ambiguity was confirmed with the use of continuous accordion pleats in the printed gradation fabric. It is anticipated that more diverse and creative designs could be created using more extended techniques in future studies.

종이접기와 점토활동이 유아의 창의성과 언어능력에 미치는 효과 비교

이승임,지성애 한국영유아교원교육학회 2004 유아교육학논집 Vol.8 No.4

This study aims to compare the educational value of paper folding and clay activities by determining the effects of paper folding and clay activities on children’s creativity and language ability and develop programs for paper folding and clay activities. The participants in this study consist of 41 five-year-old children attending kindergartens attached to D elementary school and N elementary school, respectively, in Naju-city, Jeollanamdo, Korea. Test instruments used in this research are the Chilgyopan Creativity Test by Sang Yun, Kim (2000) to measure creativity, and the Expressive One-Word Picture Vocabulary Test-revised version by Gardner (1990) to measure language ability. Both tests were used as instruments for pretest and posttest. The results of this research are as follows.:First, it is found that the experimental group, which conducted paper folding, showed significantly higher improvements in creativity than the comparative group, which did clay activities. Second, it is found that the comparative group, which conducted clay activities, showed significantly higher improvements in language ability than the experimental group, which did paper folding. In conclusion, paper folding is more effective than clay activities in improving children’s creativity, whereas clay activities are more effective than paper folding in improving children’s language ability. The results of this study suggest that paper folding and clay activities should be used in field education in a systematic and concrete way. 본 연구는 종이접기와 점토활동이 유아의 창의성과 언어능력에 어떠한 영향을 미치는지 비교함으로써, 종이접기와 점토활동의 교육적 가치를 재조명해 보고, 유아교육 현장에 종이접기와 점토활동을 효과적으로 활용할 수 있는 방안을 모색해 보고자 하였다. 만 5세 유아 41명을 대상으로 4주간의 실험처치(12회)로 실험집단에는 종이접기 활동을 비교집단에는 점토활동을 실시한 결과, 종이접기를 실시한 실험집단 유아들이 점토활동을 실시한 비교집단 유아들보다 창의성이 유의하게 높게 나타났다. 이에 반해 점토활동을 실시한 비교집단 유아들이 종이접기를 실시한 실험집단 유아들보다 언어능력이 유의하게 높은 것으로 드러났다.

새로운 디지털 인코딩 기법을 적용한 8비트 1GS / s 프랙셔널 폴딩 - 인터폴레이션 ADC

최동귀(Donggwi Choi),김대윤(Daeyun Kim),송민규(Minkyu Song) 대한전자공학회 2013 전자공학회논문지 Vol.50 No.1