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This paper presents synthesis of vancomycin derivatives modified with selected 1- and 2-aminoalditols to carboxylic function and 2,5-anhydro-D-mannose and D-talose to amino function of vancosamine via reductive alkylation. MIC and MBC of these derivatives were determined for reference strains of bacteria: Staphylococcus aureus ATCC 25923, ATCC 6538, ATCC 6538/P, S. epidemidis ATCC 14490, E. faecium PCM 1859, E. faecalis PCM 2673, S. pyogenes PCM 465, and S. pneumonia ATCC 49619 and compared with the activity of vancomycin and its aglycone. Our findings confirm that sugar fragments can play an important role in the mechanism of interaction of vancomycin with bacterial cell wall peptidoglycan.

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands., Cancer Research UK, Grant/Award Number: FC001003; Changzhou Science and Technology Bureau, Grant/Award Number: CE20200503; Department of Energy and Climate Change, Grant/Award Numbers: DE-AR001213, DE-SC0020400, DE-SC0021303; H2020 European Institute of Innovation and Technology, Grant/Award Numbers: 675728, 777536, 823830; Institut national de recherche en informatique et en automatique (INRIA), Grant/Award Number: Cordi-S; Lietuvos Mokslo Taryba, Grant/Award Numbers: S-MIP-17-60, S-MIP-21-35; Medical Research Council, Grant/Award Number: FC001003; Japan Society for the Promotion of Science KAKENHI, Grant/Award Number: JP19J00950; Ministerio de Ciencia e Innovación, Grant/Award Number: PID2019-110167RB-I00; Narodowe Centrum Nauki, Grant/Award Numbers: UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, UMO-2017/27/B/ST4/00926; National Institute of General Medical Sciences, Grant/Award Numbers: R21GM127952, R35GM118078, RM1135136, T32GM132024; National Institutes of Health, Grant/Award Numbers: R01GM074255, R01GM078221, R01GM093123, R01GM109980, R01GM133840, R01GN123055, R01HL142301, R35GM124952, R35GM136409; National Natural Science Foundation of China, Grant/Award Number: 81603152; National Science Foundation, Grant/Award Numbers: AF1645512, CCF1943008, CMMI1825941, DBI1759277, DBI1759934, DBI1917263, DBI20036350, IIS1763246, MCB1925643; NWO, Grant/Award Number: TOP-PUNT 718.015.001; Wellcome Trust, Grant/Award Number: FC001003

The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab initio, contact-assisted, and data-assisted modes. Significant improvement of the performance has been observed with respect to the CASP11 and CASP12 experiments (by over 10 GDT_TS units for the ab initio mode predictions and by over 15 GDT_TS units for the contact-assisted prediction, respectively), which is a result of introducing scale-consistent terms and improved handling of contact-distance restraints. As in previous CASP exercises, UNRES ranked higher in the free modeling category than in the general category that included template based modeling targets. Use of distance restraints from the predicted contacts, albeit many of them were wrong, resulted in the increase of GDT_TS by over 8 units on average and introducing sparse restraints from small-angle X-ray/neutron scattering and chemical cross-link-mass-spectrometry experiments, and ambiguous restraints from nuclear magnetic resonance experiments has also improved the predictions by 8.6, 9.7, and 10.7 GDT_TS units on average, respectively.

The physics-based UNRES coarse-grained force field for the simulations of protein structure and dynamics has been extended to treat membrane proteins. The lipid bilayer has been modeled by introducing a continuous nonpolar phase with the water-interface region of appropriate thickness. The potentials for average electrostatic and correlation interactions of the peptide groups have been rescaled to account for the reduction of the dielectric permittivity compared to the water phase and new potentials for protein side-chain-side-chain interactions inside and across the lipid phase have been introduced. The model was implemented in the UNRES package for coarse-grained simulations of proteins, and the package with the new functionality was tested for total energy conservation and thermostat behavior in microcanonical and canonical molecular dynamics simulations runs, respectively. The method was validated by running unrestricted ab initio blind-prediction tests of 10 short α-helical membrane proteins, all runs started from the extended structures. The modified UNRES force field was able to predict correctly the overall folds of the membrane proteins studied.

The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES-contact group), and (iii) template-assisted (the UNRES-template group). For most of the targets, the contact restraints were derived from the server models top-ranked by the DeepQA method, while the DNCON2 method was used for 11 targets. Our consensus-fragment procedure was used to run template-assisted predictions. Each group also processed the Nuclear Magnetic Resonance (NMR)- and Small Angle X-Ray Scattering (SAXS)-data assisted targets. The average Global Distance Test Total Score (GDT_TS) of the ‘Model 1’ predictions were 29.17, 39.32, and 56.37 for the UNRES, UNRES-contact, and UNRES-template predictions, respectively, increasing by 0.53, 2.24, and 3.76, respectively, compared to CASP13. It was also found that the GDT_TS of the UNRES models obtained in ab initio mode and in the contact-assisted mode decreases with the square root of chain length, while the exponent in this relationship is 0.20 for the UNRES-template group models and 0.11 for the best performing AlphaFold2 models, which suggests that incorporation of database information, which stems from protein evolution, brings in long-range correlations, thus enabling the correction of force-field inaccuracies.

The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13). The method implements restraints from the consensus fragments common to server models. In this work, the server models to derive fragments have been chosen on the basis of quality assessment; a fully automatic fragment-selection procedure has been introduced, and Dynamic Fragment Assembly pseudopotentials have been fully implemented. The Global Distance Test Score (GDT_TS), averaged over our "Model 1" predictions, increased by over 10 units with respect to CASP12 for the free-modeling category to reach 40.82. Our "Model 1" predictions ranked 20 and 14 for all and free-modeling targets, respectively (upper 20.2% and 14.3% of all models submitted to CASP13 in these categories, respectively), compared to 27 (upper 21.1%) and 24 (upper 18.9%) in CASP12, respectively. For oligomeric targets, the Interface Patch Similarity (IPS) and Interface Contact Similarity (ICS) averaged over our best oligomer models increased from 0.28 to 0.36 and from 12.4 to 17.8, respectively, from CASP12 to CASP13, and top-ranking models of 2 targets (H0968 and T0997o) were obtained (none in CASP12). The improvement of our method in CASP13 over CASP12 was ascribed to the combined effect of the overall enhancement of server-model quality, our success in selecting server models and fragments to derive restraints, and improvements of the restraint and potential-energy functions.

Summary: Participating as the Cornell-Gdansk group, we have used our physics-based coarse-grained UNited RESidue (UNRES) force field to predict protein structure in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11). Our methodology involved extensive multiplexed replica exchange simulations of the target proteins with a recently improved UNRES force field to provide better reproductions of the local structures of polypeptide chains. All simulations were started from fully extended polypeptide chains, and no external information was included in the simulation process except for weak restraints on secondary structure to enable us to finish each prediction within the allowed 3-week time window. Because of simplified UNRES representation of polypeptide chains, use of enhanced sampling methods, code optimization and parallelization and sufficient computational resources, we were able to treat, for the first time, all 55 human prediction targets with sizes from 44 to 595 amino acid residues, the average size being 251 residues. Complete structures of six single-domain proteins were predicted accurately, with the highest accuracy being attained for the T0769, for which the CαRMSD was 3.8 Å for 97 residues of the experimental structure. Correct structures were also predicted for 13 domains of multi-domain proteins with accuracy comparable to that of the best template-based modeling methods. With further improvements of the UNRES force field that are now underway, our physics-based coarse-grained approach to protein-structure prediction will eventually reach global prediction capacity and, consequently, reliability in simulating protein structure and dynamics that are important in biochemical processes. Availability and Implementation: Freely available on the web at http://www.unres.pl/ . Contact: has5@cornell.edu

Solid phase peptide synthesis (SPPS) of two selected muramyl pentapeptide derivatives is described. The simplicity of removing the protecting groups via one-step deprotection and cleavage from the resin is the biggest advantage of SPPS. Using this method, two muramyl pentapeptide derivatives, D-MurN3-L-Ala-D-iGlu-L-Lys-D-Ala-D-Ser (5) and D-MurN3-L-Ala-D-iGlu-L-Lys-D-Ala-D-Ala (6), were obtained. Their chemical structures were confirmed by high-resolution mass spectrometry (HRMS) and nuclear magnetic resonance (NMR) spectroscopy. To determine the absolute configuration of the carbon atom in the side chain of the muramic acid derivative, single-crystal X-ray diffraction measurements were recorded.

Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research. Funding Agencies|Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Visiting Faculty Program (VFP); United States-Israel Binational Science Foundation (BSF) [2009432]; Israel Science Foundation (ISF) [1122/14]; National Institute of General Medical Sciences [R01GM093123, GM083107, GM116960]; Purdue University start-up funds; Ralph W. and Grace M. Showalter Trust Award; Jim and Diann Robbers Cancer Research Grant for New Investigators Award; Brazilian agency: FAPESP; Brazilian agency: CAPES; Brazilian agency: CNPq; NIH [GM-14312]; NSF [MCB-10-19767]; National Institutes of Medicine [GM11574901]; Swedish Research Council [2012-5270, 2016-05369]; Swedish e-Science Research Center; Polish National Science Center [UMO-2013/10/M/ST4/00640]; IISc Mathematical Initiative Assistantship; National Academy of Sciences, India; National Institutes of Health [R01-GM100701, R01GM052032]; National Science Foundation; National Science Foundation Graduate Research Fellowship [DGE-1148900]; Princeton Institute for Computational Science and Engineering (PICSciE); Princeton University Office of Information Technology; UK Engineering and Physical Sciences Research Council [EP/M020576/1, EP/N031962/1]; National Research Foundation of Korea [2016R1A2A1A05005485]

Trypsin inhibitor SFTI-1 is the smallest and the most potent among BBI inhibitors. It is also an interesting object for SAR studies since it is cyclic 14 amino acid molecule which additionally contains disulfide bridge. We showed that elimination of head-to-tail cycliztion did not influence its activity. Moreover peptoid monomers of Nlys and Nphe introduced in the substrate specificity P1 position of monocyclic SFTI-1 preserved trypsin and chymotripsin inhibitory activity respectively and made P1–P1′ bond proteolytically stable. These findings motivated us to perform conformational analysis of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy and molecular dynamics calculations. Obtained structure occurred to be in a good agreement with published structures for wild-type SFTI-1, its monocyclic analog with disulfide bridge only as well as one containing Nlys peptoid monomer in P1 position.

Knowledge-based methods are, at present, the most effective ones for the prediction of protein structures; however, their results heavily depend on the similarity of a target sequence to those of proteins with known structures. On the other hand, the physics-based methods, although still less accurate and more expensive to execute, are independent of databases and give reasonable results where the knowledge-based methods fail because of weak sequence similarity. Therefore, a plausible approach seems to be the use of knowledge-based methods to determine the sections of the structures that correspond to sufficient sequence similarity and physics-based methods to determine the remaining structure. By participating in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12) as the KIAS-Gdansk group, we tested our recently developed hybrid approach, in which protein-structure prediction is carried out by using the physics-based UNRES coarse-grained energy function, with restraints derived from the server models. Best predictions among all groups were obtained for 2 targets and 80% of our models were in the upper 50% of the models submitted to CASP. Our method was also able to exclude, with about 70% confidence, the information from the servers that performed poorly on a given target. Moreover, the method resulted in the best models of 2 refinement targets and performed remarkably well on oligomeric targets.

Proper understanding of the mechanisms of binding to Gram-positive bacteria cell wall layers-especially to the peptidoglycan (PG) layer, seems to be crucial for proper development of new drug candidates which are effective against these bacteria. In this work we have constructed two different models of the Gram-positive bacteria PG layer: the layered and the scaffold models. PG conformational changes during geometry optimization, models relaxation, and molecular dynamics were described and discussed. We have found that the border surface of both PG layer models differs from the surface located away from the edge of models and the chains formed by disaccharide units prefer helix-like conformation. This curling of PG chains significantly affects the shape of antibiotic-accessible surface and the process is thus crucial for new drug development. Glycopeptide antibiotics effective against Gram-positive bacteria, such as vancomycin and its semisynthetic derivatives-oritavancin and telavancin, bind to d-alanyl-d-alanine stem termini on the peptidoglycan precursors of the cell wall. This binding inhibits cross-linking between the peptides and subsequently prevents cell wall synthesis. In this study some of the aspects of conformational freedom of vancomycin and restrictions from the modifications of vancomycin structure introduced into oritavancin and telavancin and five other vancomycin derivatives (with addition of 2-acetamido-2-deoxy-β-d-galactopyranosylamine, 2-acetamido-2-deoxy-β-d-glucopyranosylamine, 1-amine-1-deoxy-d-glucitol, 2-amino-2-deoxy-d-galactitol, or 2-amino-2-deoxy-d-glucitol to the C-terminal amino acid group in the vancomycin) are presented and discussed. The resulting molecular dynamics trajectories, root mean square deviation changes of aglycon and saccharide moieties as well as a comparative study of possible interactions with cyclic and chain forms of modified groups have been carried out, measured, and analyzed. Energetically advantageous conformations show close similarity to the structures known from the experimental data, but the diversity of others suggest very high conformational freedom of all modeled antibiotics and vancomycin derivatives. Alditol derivatives move closer to the peptidoglycan chain more easily but they also form intramolecular interactions more frequently than their homologous cyclic forms. One of the proposed derivatives seems to be a promising agent which is efficient in treatment of infections caused by Gram-positive bacteria.

Computational investigations were performed to examine the effects of the addition of 2-acetamido-2-deoxy-β-D-galactopyranosylamine or 1-amino-1-deoxy-D-glucitol connected to the C-terminus of vancomycin with different linkers. The purpose of this modification was to find more effective vancomycin derivatives by providing alternative interactions between vancomycin moiety and the peptidoglycan precursor. Each prepared vancomycin–peptidoglycan complex was optimized and submitted to the molecular dynamics study and analysis. The analysis of overall root mean square deviation, changes in position and interactions involving modified part of vancomycin as well as cluster analysis were carried out. One of the proposed vancomycin analogues seems to be efficient vancomycin substitute.

Six complexes of vancomycin and peptidoglycan precursors were studied via molecular dynamics simulations. The interactions between the antibiotic and peptidoglycan fragments were identified and described in detail. All six studied modifications of the peptidoglycan precursor resulted in a weakening of the interaction with vancomycin when comparing to the native D-Ala-D-Ala-terminated fragment. It was confirmed that the N-terminus of the vancomycin is directly responsible for peptidoglycan recognition and antimicrobial activity. In simulated systems, the saccharide part of the antibiotic interacts with peptide precursors, thus it could also be important for antimicrobial activity. The complex terminated with D-Lac is the only one in which there is a weak interaction with the sugar moiety in the simulated systems. Analysis of conformational changes is a major scope of this work. The lack of interactions resulting from modification of the peptidoglycan precursors (D-Lac, D-Ser or other substitution) would be counterbalanced by proper modifications of the vancomycin moiety, especially the saccharide part of vancomycin.

In this paper we use NMR spectroscopy and molecular modeling to examine four vasopressin analogues substituted with bulky 3,3'-diphenylalanine (Dpa) enantiomers: [Mpa(1),Dpa(2),Val(4),D-Arg(8)]VP (I), [Mpa(1),D-Dpa(2),Val(4),D-Arg(8)]VP (II), [D-Dpa(2),D-Arg(8)]VP (III) and [Mpa(1),D-Dpa(2)]AVP (IV). All the peptides exhibit a strong and prolonged antidiuretic activity. Additionally, analogues II, III and IV display antiuterotonic activity and analogue II is also a weak V(1a) receptor blocker. The conformational analysis has shown that beta-turns at positions 2,3 and/or 3,4 are characteristic of OT antagonists. In turn, the beta-turn in the Cys(6)-Gly(9) fragment seems to be crucial for enhancement of the antidiuretic activity. The high accessibility of aromatic side chains at positions 2 and 3 plays a crucial role in antagonist-receptor binding. Moreover, orientation of the Phe(3) side chain is claimed to be important for V(1a) receptor affinity.

The Escherichia coli heat shock protein ClpB, a member of the Hsp100 family, plays a crucial role in cellular thermotolerance. In co-operation with the Hsp70 chaperone system, it is able to solubilize proteins aggregated by heat shock conditions and refold them into the native state in an ATP-dependent way. It was established that the mechanism of ClpB action depends on the formation of a ring-shaped hexameric structure and the translocation of a protein substrate through an axial channel. The structural aspects of this process are not fully known. By means of homology modeling and protein-protein docking, we obtained a model of the hexameric arrangement of the full-length ClpB protein complexed with ATP. A molecular dynamics simulation of this model was performed to assess its flexibility and conformational stability. The high mobility of the "linker" M-domain, essential for the renaturing activity of ClpB, was demonstrated, and the size and shape of central channel were analyzed. In this model, we propose the coordinates for a loop between b4 and B6 structural elements, not defined in previous structural research, which faces the inside of the channel and may therefore play a role in substrate translocation.

In this work, the receptor-bound conformation of nine vasopressin (CYFQNCPRG-NH2, AVP) analogs substituted in positions 2 or 3 with 2-aminoindane-2-carboxylic acid have been investigated using molecular modeling methods. The synthesis and functional assays of the analogs have been recently described. For comparison, the molecular dynamics of the selected analogs has been conducted. We have observed the relationship between the value of valence angle between the aromatic rings in positions 2 and 3 and the biological activity of the analogs. Both, in restricted space of the receptor cavities and unlimited continuous water environment, the same valence angles prevail, thus seem to be energetically more favorable for the particular peptides. Moreover, the residues responsible for analogs binding to the receptors have been identified.

Conformational studies of three agonists of V2 receptor modified with 1-aminocyclohexane-1-carboxylic acid (Acc), [Acc2,DArg8]VP, [Acc3]AVP and [Cpa1,Acc3]AVP, using 2D NMR and theoretical calculations are presented in this paper. It is believed that α,α-disubstituted amino acids, such as Acc, affect the formation of either 310 or α-helical conformation. Moreover, a peptide with Acc may adopt either the γ- or an inverse γ-turn over it. Thus, incorporation of Acc into the arginine-vasopressin sequence induced C7-membered ring conformation with Acc at the top of it, and additional formation of β-bend involving residues in the 2–5 fragment of the peptides. Furthermore, the analogues are also characterized by type I of β-turn involving residues Acc3-Cys6 in [Acc3]AVP and [Cpa1,Acc3]AVP, and by type IV or II′ in [Acc2,DArg8]VP. Replacement of Tyr at position 2 of [Acc2,DArg8]VP with Acc afforded a hydrogen bond between the guanidine moiety of DArg8 and the side chain of either Asn5 or Gln4. In the remaining analogues, the β-turn comprising the Cys6-Gly9 residues allows the positively charged side chain of Arg8 to be directed toward Tyr2. The substitution of Cys1 with Cpa1 enhances hydrophobic properties of N-terminal part of the molecule strengthening thereby the affinity to the binding pocket of receptors.

In the Arginine Vasopressin (CYFQNCPRG–NH2, AVP) molecule, the disulfide bond between Cys1 and Cys6 forms a 20-membered ring crucial for AVP activity. The activity could be enhanced by restraining the AVP structure with additional cyclic moiety. To reduce AVP conformational flexibility, a standard link has now been added between residues at position 4, substituted with different positively charged amino acids, and Gly at position 9. The resulting AVP analogues have subsequently been docked to the vasopressin and oxytocin receptors and relaxed/geometry optimized using a Constrained Simulated Annealing (CSA) procedure. The results of our modeling suggest that the size of the additional AVP cycle is crucial for the biological activity of the analogue.

A model believed to be representative for activated class A G protein-coupled receptors is proposed. It consists of rhodopsin and the transducin a C-terminal peptide [Gta(338 -350)] docked to it. The model utilizes the resolved interactions/distances, found to be essential in the activated rhodopsin (RD*) and the structure of Gta(338-350) that is known to stabilize RD*. Long-term molecular dynamics (14.8 ns) in fully hydrated lipid bilayer model is applied to the system to refine and verify conformational changes in rhodopsin itself and the structure of the complex. A concomitant role of Gta and Gtγ C-termini in stabilizing RD* could possibly be resolved assuming a receptor dimer as a requisite for G protein activation.

The nonapeptide hormone oxytocin CYIQNCPLG-NH 2 (OT) controls birth, lactation and other physiological functions in the mammals via stimulation of its receptor (OTR), a member of Class A G protein-coupled receptors (GPCRs). OT is structurally akin to arginine vasopressin ([F2,R8]OT, AVP) involved, among other things, in the increase of blood pressure and antidiuresis via related V1a and V2 receptors (V1aR and V2R), respectively. Barusiban - [Mpa 1 -D-Trp 2 -Ile 3 -allo-Ile 4 -Asn5-Abu 6 -Mol 7 ], FE200 440 - a potent and selective OT antagonist, appears promising in preventing from premature birth. In this work, molecular modeling of barusiban complexes with OTR, V1aR and V2R is described. The modeling consists of: (1) ligand-receptor docking; (2) selection of two best complexes per each receptor, based on energetic and other criteria; and (3) relaxation of the latter by 1-ns molecular dynamics (MD) in the fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer. The comparison of the ligand-host interactions among the three types of MD-relaxed barusiban-receptor complexes, leads to a hypothesis that it is a unique interaction involving the ligand D-Trp 2 in the barusiban-OTR system that could be responsible for the potency and selectivity of the antagonist. The hypothesis, that barusiban might be an inverse agonist of OTR is advanced. The finding is experimentally verifiable and if true, it may be helpful in devising new valuable OTR, VlaR and V2R antagonists.

The aim of our research was to get insight into the molecular mechanism of binding atosiban, a strong selective oxytocin (OT) antagonist by OT receptor (OTR) versus vasopressin V1a and V2 receptors (VlaR and V2R, respectively). The docking of ligand and interaction with receptor are dynamic events and Molecular Dynamics (MD) seems to be a proper tool for studying the mentioned processes. Therefore we describe MD of three pairs of atosiban-receptor complexes, two complexes per each receptor, conducted in the fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline lipid bilayer, simulating G protein-coupled receptors environment. We confirmed strong and specific binding of atosiban in OTR and a weaker binding of it in VlaR, on the contrary to its less specific binding in V2R, in the agreement with our preliminary results [Slusarz et al. 2003].

In this study the interaction of seven new analogs of arginine vasopressin (AVP) substituted in position 2 or 3 with 1-aminocyclohexanecarboxylic acid (Acc) with the vasopressin (VP) and oxytocin (OT) receptors (V 1 a R, V 2 R and OTR) is described. All peptides were synthesized and tested in bioassays for pressor and antidiuretic activities. Also their uterotonic activity in vitro has been measured. This work was aimed at checking the applicability of computational methods for predicting receptor-ligand interactions and makes a good basis for selecting the receptor amino acid residues involved in ligand binding. The results of this study suggest preferred geometries of new, potentially active AVP analogs.

Introduction of the naphthylalanine residue into either position 3 of arginine vasopressin (AVP), or its analogs results in peptides with interesting pharmacological properties. The single substituted analog of AVP with L-2-Nal in position 3 causes moderate antiduretic activity, whereas [Mpa1, (L-1-Nal)3, (D-Arg)8] VP and [Mpa1, (L-2-Nal)3, (D-Arg)8] VP are potent and selective V2 agonists. Moreover [(L-2-Nal)3, (D-Arg)8] VP is among the most potent and selective antagonists of V1a receptors. In this study we carried out conformational calculations on [(L-1-Nal)3] AVP, [(L-2-Nal)3] AVP, [(L-1-Nal)3, (D-Arg)8] VP, [(L-2-Nal)3, (D-Arg)8] VP, [Mpa1, (L-1-Nal)3, (D-Arg)8] VP, [Mpa1, (L-2-Nal)3, (D-Arg)8] VP, using the ECEPP/3 force field with and without including hydration to simulate aqueous and nonpolar environments. It was found that in all six compound studied, the low-energy conformations have common geometry and relative energies. Therefore, the modifications of the Phe in position 3 influence the binding to the receptor by changing the size of the third residue, rather than by changing the conformational space. The lowest-energy conformations in the presence and absence of water had beta-turns at residues Phe3-Gln4 and Gln4-Asn5 and Gln4-Asn5, respectively. The conformation at the Gln4-Asn5 turn was most similar to the crystal structure of the pressinoic acid (the cyclic moiety of vasopressin).

A unified coarse-grained model of three major classes of biological molecules—proteins, nucleic acids, and polysaccharides—has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point multipoles. The model is an extension of the united residue (UNRES) coarse-grained model of proteins developed previously in our laboratory. The respective force fields are defined as the potentials of mean force of biomacromolecules immersed in water, where all degrees of freedom not considered in the model have been averaged out. Reducing the representation to one center per polar interaction site leads to the representation of average site–site interactions as mean-field dipole–dipole interactions. Further expansion of the potentials of mean force of biopolymer chains into Kubo’s cluster-cumulant series leads to the appearance of mean-field dipole–dipole interactions, averaged in the context of local interactions within a biopolymer unit. These mean-field interactions account for the formation of regular structures encountered in biomacromolecules, e.g., α-helices and β-sheets in proteins, double helices in nucleic acids, and helicoidally packed structures in polysaccharides, which enables us to use a greatly reduced number of interacting sites without sacrificing the ability to reproduce the correct architecture. This reduction results in an extension of the simulation timescale by more than four orders of magnitude compared to the all-atom representation. Examples of the performance of the model are presented. Figure Components of the Unified Coarse Grained Model (UCGM) of biological macromolecules

The performance of the physics-based protocol, whose main component is the United Residue (UNRES) physics-based coarse-grained force field, developed in our laboratory for the prediction of protein structure from amino acid sequence, is illustrated. Candidate models are selected, based on probabilities of the conformational families determined by multiplexed replica-exchange simulations, from the 10th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP10). For target T0663, classified as a new fold, which consists of two domains homologous to those of known proteins, UNRES predicted the correct symmetry of packing, in which the domains are rotated with respect to each other by 180° in the experimental structure. By contrast, models obtained by knowledge-based methods, in which each domain is modeled very accurately but not rotated, resulted in incorrect packing. Two UNRES models of this target were featured by the assessors. Correct domain packing was also predicted by UNRES for the homologous target T0644, which has a similar structure to that of T0663, except that the two domains are not rotated. Predictions for two other targets, T0668 and T0684_D2, are among the best ones by global distance test score. These results suggest that our physics-based method has substantial predictive power. In particular, it has the ability to predict domain-domain orientations, which is a significant advance in the state of the art.

Vasopressin (CYFQNCPRG-NH2, AVP) is a semicyclic endogenous peptide, which exerts a variety of biological effects in mammals. The main physiological roles of AVP are the regulation of water balance and the control of blood pressure and adrenocorticotropin hormone (ACTH) secretion, mediated via three different subtypes of vasopressin receptors: V1a, V1b and V2 receptors (V1aR, V1bR and V2R, respectively). They are the members of the class A, G-protein-coupled receptors (GPCRs). AVP also modulates several behavioral and social functions. In this study, the interactions responsible for AVP binding to vasopressin V1a and V2 receptors versus the closely related oxytocin ([I3,L8]AVP, OT) receptor (OTR) have been investigated. Three-dimensional models of the activated receptors were constructed using multiple sequence alignment, followed by homology modeling using the complex of activated rhodopsin with GtαC-terminal peptide of transducin MII-Gt(338-350) prototype as a template. AVP was docked into the receptor-Gα systems. The three lowest-energy pairs of receptor-AVP-Gα (two complexes per each receptor) were selected. The 1-ns unconstrained molecular dynamics (MD) of complexes embedded into the fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer was conducted in the AMBER 7.0 force field. Six relaxed receptor-AVP-Gα models were obtained. The residues responsible for AVP binding to vasopressin receptors have been identified and a different mechanism of AVP binding to V2R than to V1aR has been proposed. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.

The solution conformations of two potent antagonists of bradykinin (Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9), [Aca(-1),DArg0,Hyp3,Thi5,DPhe7,(N-Bzl)Gly8]BK (1) and [Aaa(-1),DArg0,Hyp3,Thi5,(2-DNal)7,Thi8]BK (2), were studied by using 2D NMR spectroscopy in DMSO-d6 and molecular dynamics simulations. The NMR spectra of peptide 1 reveals the existence of at least two isomers arising from isomerization across the DPhe7-(N-Bzl)Gly8 peptide bond. The more populated isomer possesses the cis peptide bond at this position. The ratio of cis/trans isomers amounted to 7:3. With both antagonists, the NMR data indicate a beta-turn structure for the Hyp3-Gly4 residues. In addition, for peptide 2, position 2,3 is likely to be occupied by turn-like structures. The cis peptide bond between DPhe7 and (N-Bzl)Gly8 in analogue 1 suggests type VI beta-turn at position 7,8. The molecular dynamics runs were performed on both peptides in DMSO solution. The results indicate that the structure of peptide 1 is characterized by type VIb beta-turn comprising residues Ser6-Arg9 and the betaI or betaII-turn involving the Pro2-Thi5 fragment, whereas peptide 2 shows the tendency towards the formation of type I beta-turn at position 2,3. The structures of both antagonists are stabilized by a salt bridge between the guanidine moiety of Arg1 and the carboxyl group of Arg9. Moreover, the side chain of DArg0 is apart of the rest of molecule and is not involved in structural elements except for a few calculated structures.

The solution conformation of vasopressin analogues, modified at positions 2 and 3 with N-methylphenylalanine or its enantiomer, [D-MePhe2,MePhe3]AVP and [MePhe2,D-MePhe3]AVP, were studied by 2D NMR spectroscopy in H2O/D2O and theoretical calculations (EDMC/ANALYZE). In the case of [MePhe2,D-MePhe3]AVP, the synthesis afforded two products, A and B, which had identical molecular ions and similar retention times on HPLC. This finding was explained by racemization of Cys1, which gave an additional analogue, [D-Cys1,MePhe2,D-MePhe3]AVP (B). The possibility is not excluded of racemization of Cys1 in the remaining analogues of this series. However, only in the case of [MePhe2,D-MePhe3]AVP was this process so distinct that two strong peaks in the HPLC chromatogram were observed. The NMR spectra of all the analogues showed several distinct sets of residual proton resonances. This suggests that the peptides adopt more than two groups of conformations in H2O/D2O. This fact is due to cis/trans isomerization. Two more populated isomers arise from the cis/trans isomerization across the 2–3 peptide bond in [D-MePhe2,MePhe3]AVP and [MePhe2,D-MePhe3]AVP (A) and across the 1–2 peptide bond in [D-Cys1,MePhe2,D-MePhe3]AVP (B). Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.

Growing evidence that rhodopsin (RD) and related G protein-coupled receptors form functional dimers/oligomers, followed by direct proof (using atomic force microscopy) that in the retina disc membrane RD associates into a paracrystalline network of rows of dimers, need models of the RD-transducin (Gt) complex that would envision an optimal RD dimer/oligomer able to satisfy all well-documented interactions with Gt. Of the models proposed so far, only a few refer to RD dimers and only one of them proposes a complex of Gt with an RD oligomer (Filipek S, Krzyśko KA, Fotiadis D, Liang Y, Saperstein DA, Engel, A, Palczewski K Photochem Photobiol Sci 3: 628–638, 2004). This paper puts forward a hypothesis on another arrangement of RD monomers into the reported network of rows of dimers. Arguments for the compatibility of this set-up with interactions and activation of RD in the complex with Gt, in particular, with the well-documented movement of transmembrane helix 6 and cytosolic loop 3, which is vital for RD activation, are provided and discussed.

G protein-coupled receptors relay diverse extracellular signals into cells via a common mechanism, involving activation of cytosol G proteins. The mechanism underlies the actions of approximately 50% of all drugs. In this work, we focus on simulating three protein-ligand complexes of the neurohypophyseal hormone analog 4-OH-phenylacetyl- D-Y(Me)FQNRPR-NH2 (I) with the human V1a, V2 and oxytocin receptors. The peptideI is a potent selective V1a receptor antagonist. To obtain relaxed models of the complexes, the following techniques were used: docking ofI into the vasopressin V1a, V2 and oxytocin receptor models, optimization of the geometry of the resulting complexes and molecular dynamics in a fully hydrated 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphatidylcholine lipid bilayer. The results of the simulations allow us to draw some conclusions about the ligand selectivity to V1aR.

Hepta-helical transmembrane receptors transducing diverse external signals to cells via activation of heterotrimeric GTP-binding proteins (G-proteins), estimated to occupy over 3% of our genome [1] and to mediate actions of 60% of drugs [2], had long been resistant to structure determination. Thus, the first 3D structure of a G protein-coupled receptor (GPCR) dark rhodopsin (RD) [3], is a landmark event as it provides at last a trustworthy 3D prototype for the inactive (antagonist-bound) form of this huge family of proteins. Our interest in mechanisms of signal transduction by three other GPCRs, i.e., vasopressin pressor, antidiuretic, and oxytocin receptors (V1aR, V2R and OTR, respectively) thus needs a verification of the models. Of a few theoretical GPCR templates [4–6], our recent favorite was based on the robust assumption, simultaneously applied to 400 sequences, that if intra-molecular particular polar interactions were maximized, the TM-bundles would converge to a realistic common 3D pattern [4].