High accuracy template based modeling by global optimization

Joo, Keehyoung,Lee, Jinwoo,Lee, Sunjoong,Seo, Joo-Hyun,Lee, Sung Jong,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2007 Proteins Vol. No.

<P>For high-accuracy template-based-modeling of CASP7 targets, we have applied a procedure based on the rigorous optimization of score functions at three stages: multiple alignment, chain building, and side-chain modeling. We applied the conformational space annealing method to a newly developed consistency based score function for multiple alignment. For chain building, we optimized the MODELLER energy function. For side-chain modeling, we optimized a SCWRL-like energy function using a rotamer library constructed specifically for a given target sequence. By rigorous optimization, we have achieved significant improvement in backbone as well as side-chain modeling for TBM and TBM/HA targets. For most TBM/HA targets (17/26), the predicted model was more accurate than the model one can construct from the best template in a posteriori fashion. It appears that the current method can extract relevant information out of multiple templates. Proteins 2007. © 2007 Wiley-Liss, Inc.</P>

Prediction of Protein Secondary Structure Using PREDICT, a Nearest Neighbor Method on Pattern Space

Keehyoung Joo,Jooyoung Lee,Ilsoo Kim,Julian Lee,Seung-Yeon Kim,Sung Jong Lee 한국물리학회 2004 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.45 No.3

We introduce a novel method for predicting the secondary structure of proteins, PREDICT (PRofile Enumeration DICTionary), in which the nearest-neighbor method is applied to a pattern space. For a given protein sequence, PSI-BLAST is used to generate a prole that denes patterns for amino acid residues and their local sequence environments. By applying the PSI-BLAST to protein sequences with known secondary structures, we construct pattern databases. The secondary structure of a query residue of a protein with unknown structure can be determined by comparing the query pattern with those in the pattern databases and selecting the patterns close to the query pattern. We have tested the PREDICT on the CB513 set (a set of 513 non-homologous proteins) in three dierent ways. The rst test was based on a pattern database derived from 7777 proteins in the Protein Data Bank (PDB), including those homologous to proteins in the CB513 set and gave an average Q3 score of 78.8 % per chain. In the second test, in order to carry out a more stringent benchmark test on the CB513 set, we removed from the 7777 proteins all proteins homologous to the CB513 set, leaving 4330 proteins. Pattern databases were constructed based on these proteins, and the average Q3 score was 74.6 %. In the third test, we selected one query protein among the CB513 set and built pattern databases by using the remaining 512 proteins. This procedure was repeated for each of the 513 proteins, and the average Q3 score was 73.1 %. Finally, we participated in the CASP5 (group ID: 531) where we employed the rst-layer database based on the 7777 proteins and the second-layer database based on the CB513 set. The PREDICT gave quite promising results with an average Q3 (Sov) score of 78.1 (77.4) % on 55 CASP5 targets.

Sann: Solvent accessibility prediction of proteins by nearest neighbor method

Joo, Keehyoung,Lee, Sung Jong,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2012 Proteins Vol.80 No.7

<P><B>Abstract</B></P><P>We present a method to predict the solvent accessibility of proteins which is based on a nearest neighbor method applied to the sequence profiles. Using the method, continuous real‐value prediction as well as two‐state and three‐state discrete predictions can be obtained. The method utilizes the <I>z</I>‐score value of the distance measure in the feature vector space to estimate the relative contribution among the <I>k</I>‐nearest neighbors for prediction of the discrete and continuous solvent accessibility. The Solvent accessibility database is constructed from 5717 proteins extracted from PISCES culling server with the cutoff of 25% sequence identities. Using optimal parameters, the prediction accuracies (for discrete predictions) of 78.38% (two‐state prediction with the threshold of 25%), 65.1% (three‐state prediction with the thresholds of 9 and 36%), and the Pearson correlation coefficient (between the predicted and true RSA's for continuous prediction) of 0.676 are achieved An independent benchmark test was performed with the CASP8 targets where we find that the proposed method outperforms existing methods. The prediction accuracies are 80.89% (for two state prediction with the threshold of 25%), 67.58% (three‐state prediction), and the Pearson correlation coefficient of 0.727 (for continuous prediction) with mean absolute error of 0.148. We have also investigated the effect of increasing database sizes on the prediction accuracy, where additional improvement in the accuracy is observed as the database size increases. The SANN web server is available at http://lee.kias.re.kr/∼newton/sann/.Proteins 2012; © 2012 Wiley Periodicals, Inc.</P>

All-atom chain-building by optimizing MODELLER energy function using conformational space annealing

Joo, Keehyoung,Lee, Jinwoo,Seo, Joo-Hyun,Lee, Kyoungrim,Kim, Byung-Gee,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol.75 No.4

<P>We have investigated the effect of rigorous optimization of the MODELLER energy function for possible improvement in protein all-atom chain-building. For this we applied the global optimization method called conformational space annealing (CSA) to the standard MODELLER procedure to achieve better energy optimization than what MODELLER provides. The method, which we call MODELLERCSA, is tested on two benchmark sets. The first is the 298 proteins taken from the HOMSTRAD multiple alignment set. By simply optimizing the MODELLER energy function, we observe significant improvement in side-chain modeling, where MODELLERCSA provides about 10.7% (14.5%) improvement for χ<SUB>1</SUB> (χ<SUB>1</SUB> + χ<SUB>2</SUB>) accuracy compared to the standard MODELLER modeling. The improvement of backbone accuracy by MODELLERCSA is shown to be less prominent, and a similar improvement can be achieved by simply generating many standard MODELLER models and selecting lowest energy models. However, the level of side-chain modeling accuracy by MODELLERCSA could not be matched either by extensive MODELLER strategies, side-chain remodeling by SCWRL3, or copying unmutated rotamers. The identical procedure was successfully applied to 100 CASP7 template base modeling domains during the prediction season in a blind fashion, and the results are included here for comparison. From this study, we observe a good correlation between the MODELLER energy and the side-chain accuracy. Our findings indicate that, when a good alignment between a target protein and its templates is provided, thorough optimization of the MODELLER energy function leads to accurate all-atom models. Proteins 2009. © 2008 Wiley-Liss, Inc.</P>

Necessary and sufficient conditions for the asymmetric synthesis of chiral amines using ω‐aminotransferases

Seo, Joo‐,Hyun,Kyung, Dohyun,Joo, Keehyoung,Lee, Jooyoung,Kim, Byung‐,Gee Wiley Subscription Services, Inc., A Wiley Company 2011 Biotechnology and bioengineering Vol.108 No.2

<P><B>Abstract</B></P><P>The half reactions of ω‐aminotransferase (ω‐AT) from <I>Vibrio fluvialis</I> JS17 (ω‐AT<I>Vf</I>) were carried out using purified pyridoxal 5′‐phosphate‐enzyme (PLP‐Enz) and pyridoxamine 5′‐phosphate‐enzyme (PMP‐Enz) complexes to investigate the relative activities of substrates. In the reaction generating PMP‐Enz from PLP‐Enz using <SMALL>L</SMALL>‐alanine as an amine donor, <SMALL>L</SMALL>‐alanine showed about 70% of the initial reaction rate of (<I>S</I>)‐α‐methylbenzylamine ((<I>S</I>)‐α‐MBA). However, in the subsequent half reaction recycling PLP‐Enz from PMP‐Enz using acetophenone as an amine acceptor, acetophenone showed nearly negligible reactivity compared to pyruvate. These results indicate that the main bottleneck in the asymmetric synthesis of (<I>S</I>)‐α‐MBA lies not in the amination of PLP by alanine, but in the amination of acetophenone by PMP‐Enz, where conformational restraints of the enzyme structure is likely to be the main reason for limiting the amine group transfer from PMP‐Enz to acetophenone. Based upon those half reaction experiments using the two amino acceptors of different activity, it appears that the relative activities of the two amine donors and the two acceptors involved in the ω‐AT reactions can roughly determine the asymmetric synthesis yield of the target chiral amine compound. Predicted conversion yields of several target chiral amines were calculated and compared with the experimental conversion yields. Approximately, a positive linear correlation (Pearson's correlation coefficient = 0.92) was observed between the calculated values and the experimental conversion yields. To overcome the low (<I>S</I>)‐α‐MBA productivity of ω‐AT<I>Vf</I> caused by the possible disadvantageous structural constraints for acetophenone, new ω‐ATs showing higher affinity to benzene ring of acetophenone than ω‐AT<I>Vf</I> were computationally screened using comparative modeling and protein‐ligand docking. ω‐ATs from <I>Streptomyces avermitilis</I> MA‐4680 (SAV2612) and <I>Agrobacterium tumefaciens</I> str. C58 (Atu4761) were selected, and the two screened ω‐ATs showed higher asymmetric synthesis reaction rate of (<I>S</I>)‐α‐MBA and lower (<I>S</I>)‐α‐MBA degradation reaction rate than ω‐AT<I>Vf</I>. To verify the higher conversion yield of the variants of ω‐ATs, the reaction with 50 mM acetophenone and 50 mM alanine was performed with coupling of lactate dehydrogenase and two‐phase reaction system. SAV2612 and Atu4761 showed 70% and 59% enhanced yield in the synthesis of (<I>S</I>)‐α‐MBA compared to that of ω‐AT<I>Vf</I>, respectively. Biotechnol. Bioeng. 2011;108: 253–263. © 2010 Wiley Periodicals, Inc.</P>

Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8

Krieger, Elmar,Joo, Keehyoung,Lee, Jinwoo,Lee, Jooyoung,Raman, Srivatsan,Thompson, James,Tyka, Mike,Baker, David,Karplus, Kevin Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol.77 No.suppl9

<P>A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we describe four approaches that address this 'last mile of the protein folding problem' and have performed well during CASP8, yielding physically realistic models: YASARA, which runs molecular dynamics simulations of models in explicit solvent, using a new partly knowledge-based all atom force field derived from Amber, whose parameters have been optimized to minimize the damage done to protein crystal structures. The LEE-SERVER, which makes extensive use of conformational space annealing to create alignments, to help Modeller build physically realistic models while satisfying input restraints from templates and CHARMM stereochemistry, and to remodel the side-chains. ROSETTA, whose high resolution refinement protocol combines a physically realistic all atom force field with Monte Carlo minimization to allow the large conformational space to be sampled quickly. And finally UNDERTAKER, which creates a pool of candidate models from various templates and then optimizes them with an adaptive genetic algorithm, using a primarily empirical cost function that does not include bond angle, bond length, or other physics-like terms.</P>

Protein‐binding site prediction based on three‐dimensional protein modeling

Oh, Mina,Joo, Keehyoung,Lee, Jooyoung Wiley Subscription Services, Inc., A Wiley Company 2009 Proteins Vol. No.

<P>Structural information of a protein can guide one to understand the function of the protein, and ligand binding is one of the major biochemical functions of proteins. We have applied a two-stage template-based ligand binding site prediction method to CASP8 targets and achieved high quality results with accuracy/coverage = 70/80 (LEE). First, templates are used for protein structure modeling and then for binding site prediction by structural clustering of ligand-containing templates to the predicted protein model. Remarkably, the results are only a few percent worse than those one can obtain from native structures, which were available only after the prediction. Prediction was performed without knowing identity of ligands, and consequently, in many cases the ligand molecules used for prediction were different from the actual ligands, and yet we find that the prediction was quite successful. The current approach can be easily combined with experiments to investigate protein activities in a systematic way.</P>

Single-chain insulin analogs as an insulin agonist and their implications for receptor binding

Dongho Shin,Keehyoung Joo,Jooyoung Lee,Hang-Cheol Shin 한국구조생물학회 2015 Biodesign Vol.3 No.4

The importance of conformational change has recently become a focus for considering the mechanisms by which insulin and its receptor combine to achieve an effective ligand-receptor complex. Although the insulin structure bound to its receptor (active structure) is still unknown, there are evidences that conformational change takes place in the carboxy terminal region of the insulin B-chain on receptor binding. In the present study, we have produced various single-chain insulin analogs where C-terminus of B-chain and N-terminus of A-chain are connected by various short peptides. Significant increase of bioactivity was noticed when two pairs of dibasic residues were included as part of the connecting peptide, indicating that the distance between C-terminus of B-chain and N-terminus of A-chain changes due to the repulsive force between RR and KR residues, probably further apart than without the RR and KR residues. Protein modeling suggests that insulin and single-chain insulin analogs need to open up their receptor-binding pockets for their activities. The development of highly active single-chain insulin analog may facilitate the design of novel insulin analogs or non-peptide alternatives.

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

Lee, Juyong,Joo, Keehyoung,Brooks, Bernard R.,Lee, Jooyoung American Chemical Society 2015 Journal of chemical theory and computation Vol.11 No.7

<P>We present a new all-atom structure-based method to study protein conformational transitions using Lorentzian attractive interactions based on native structures. The variability of each native contact is estimated based on evolutionary information using a machine learning method. To test the validity of this approach, we have investigated the conformational transition of adenylate kinase (ADK). The intrinsic boundedness of the Lorentzian attractive interactions facilitated frequent conformational transitions, and consequently we were able to observe more than 1000 structural interconversions between the open and closed states of ADK out of a total of 6 μs MD simulations. ADK has three domains: the nucleoside monophosphate (NMP) binding domain, the LID-domain, and the CORE domain, which catalyze the interconversion between ATP and ADP. We identified two transition states: a more frequent LID-closed-NMP-open (TS1) state and a less frequent LID-open-NMP-closed (TS2) state. The transition was found to be symmetric in both directions via TS1. We also obtained an off-pathway metastable state that was previously observed with physics-based all-atom simulations but not with coarse-grained models. In the metastable state, the LID domain was slightly twisted and formed contacts with the NMP domain. Our model correctly identified a total of 14 out of the top 16 residues with highest fluctuation by NMR experiment, thus showing excellent agreement with experimental NMR relaxation data and overwhelmingly better results than existing models.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jctcce/2015/jctcce.2015.11.issue-7/acs.jctc.5b00268/production/images/medium/ct-2015-002683_0011.gif'></P>

Design and efficient production of bovine enterokinase light chain with higher specificity in E. coli

Chun, Haarin,Joo, Keehyoung,Lee, Jooyoung,Shin, Hang-Cheol Springer-Verlag 2011 Biotechnology letters Vol.33 No.6